Starting phenix.real_space_refine on Thu Nov 20 02:54:30 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6ee8_9039/11_2025/6ee8_9039_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/6ee8_9039/11_2025/6ee8_9039.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.92 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6ee8_9039/11_2025/6ee8_9039.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6ee8_9039/11_2025/6ee8_9039.map" model { file = "/net/cci-nas-00/data/ceres_data/6ee8_9039/11_2025/6ee8_9039_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6ee8_9039/11_2025/6ee8_9039_neut.cif" } resolution = 3.92 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.007 sd= 0.065 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 2 6.06 5 P 125 5.49 5 Mg 1 5.21 5 S 99 5.16 5 C 18270 2.51 5 N 5323 2.21 5 O 5964 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 38 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 29784 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 1716 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1716 Classifications: {'peptide': 225} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 210} Chain: "B" Number of atoms: 1759 Number of conformers: 1 Conformer: "" Number of residues, atoms: 237, 1759 Classifications: {'peptide': 237} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 14, 'TRANS': 220} Unresolved non-hydrogen bonds: 41 Unresolved non-hydrogen angles: 50 Unresolved non-hydrogen dihedrals: 32 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 1, 'GLU:plan': 4, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 38 Chain: "C" Number of atoms: 8586 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1111, 8586 Classifications: {'peptide': 1111} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PCIS': 1, 'PTRANS': 61, 'TRANS': 1048} Unresolved non-hydrogen bonds: 47 Unresolved non-hydrogen angles: 58 Unresolved non-hydrogen dihedrals: 38 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASN:plan1': 1, 'PHE:plan': 1, 'GLU:plan': 3, 'ASP:plan': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 35 Chain: "D" Number of atoms: 9873 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1266, 9873 Classifications: {'peptide': 1266} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PCIS': 3, 'PTRANS': 57, 'TRANS': 1205} Chain breaks: 2 Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 54 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 3, 'GLU:plan': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 26 Chain: "E" Number of atoms: 649 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 649 Classifications: {'peptide': 83} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 76} Chain: "F" Number of atoms: 2518 Number of conformers: 1 Conformer: "" Number of residues, atoms: 319, 2518 Classifications: {'peptide': 319} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 8, 'TRANS': 310} Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 2, 'GLU:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 19 Chain: "J" Number of atoms: 875 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 875 Classifications: {'peptide': 108} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 7, 'TRANS': 100} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "O" Number of atoms: 1336 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 1336 Classifications: {'DNA': 65} Link IDs: {'rna3p': 64} Chain: "P" Number of atoms: 1228 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 1228 Classifications: {'DNA': 60} Link IDs: {'rna3p': 59} Chain breaks: 1 Chain: "M" Number of atoms: 1241 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1241 Classifications: {'peptide': 159} Link IDs: {'CIS': 1, 'PTRANS': 4, 'TRANS': 153} Chain: "D" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 1, ' ZN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 19125 SG CYS D 891 109.432 60.877 82.960 1.00169.12 S ATOM 19692 SG CYS D 968 106.034 61.770 84.984 1.00174.51 S ATOM 19734 SG CYS D 975 106.982 63.228 81.798 1.00161.34 S ATOM 19752 SG CYS D 978 106.509 59.787 80.902 1.00164.55 S ATOM 12567 SG CYS D 60 80.575 107.049 123.762 1.00178.81 S ATOM 12585 SG CYS D 62 79.844 107.368 127.301 1.00173.66 S ATOM 12720 SG CYS D 78 82.010 104.201 126.479 1.00175.82 S Time building chain proxies: 7.03, per 1000 atoms: 0.24 Number of scatterers: 29784 At special positions: 0 Unit cell: (135.2, 180.7, 195, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 2 29.99 S 99 16.00 P 125 15.00 Mg 1 11.99 O 5964 8.00 N 5323 7.00 C 18270 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.68 Conformation dependent library (CDL) restraints added in 1.3 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN D2000 " pdb="ZN ZN D2000 " - pdb=" SG CYS D 968 " pdb="ZN ZN D2000 " - pdb=" SG CYS D 978 " pdb="ZN ZN D2000 " - pdb=" SG CYS D 891 " pdb="ZN ZN D2000 " - pdb=" SG CYS D 975 " pdb=" ZN D2001 " pdb="ZN ZN D2001 " - pdb=" SG CYS D 78 " pdb="ZN ZN D2001 " - pdb=" SG CYS D 62 " pdb="ZN ZN D2001 " - pdb=" SG CYS D 60 " Number of angles added : 6 6976 Ramachandran restraints generated. 3488 Oldfield, 0 Emsley, 3488 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6464 Finding SS restraints... Secondary structure from input PDB file: 119 helices and 44 sheets defined 42.7% alpha, 15.1% beta 56 base pairs and 101 stacking pairs defined. Time for finding SS restraints: 4.18 Creating SS restraints... Processing helix chain 'A' and resid 30 through 43 Processing helix chain 'A' and resid 72 through 81 Processing helix chain 'A' and resid 203 through 225 removed outlier: 3.785A pdb=" N ALA A 222 " --> pdb=" O LEU A 218 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 45 removed outlier: 3.910A pdb=" N ASN B 36 " --> pdb=" O TYR B 32 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N SER B 37 " --> pdb=" O THR B 33 " (cutoff:3.500A) Processing helix chain 'B' and resid 72 through 82 Processing helix chain 'B' and resid 203 through 224 removed outlier: 3.540A pdb=" N ALA B 209 " --> pdb=" O ARG B 205 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N LEU B 221 " --> pdb=" O GLU B 217 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N ALA B 222 " --> pdb=" O LEU B 218 " (cutoff:3.500A) Processing helix chain 'C' and resid 54 through 66 removed outlier: 4.443A pdb=" N SER C 60 " --> pdb=" O VAL C 56 " (cutoff:3.500A) Processing helix chain 'C' and resid 67 through 76 removed outlier: 3.570A pdb=" N ALA C 75 " --> pdb=" O ARG C 71 " (cutoff:3.500A) Processing helix chain 'C' and resid 84 through 94 Processing helix chain 'C' and resid 118 through 126 Processing helix chain 'C' and resid 233 through 242 removed outlier: 3.720A pdb=" N LEU C 237 " --> pdb=" O PRO C 233 " (cutoff:3.500A) Processing helix chain 'C' and resid 244 through 252 removed outlier: 3.954A pdb=" N ARG C 251 " --> pdb=" O GLN C 247 " (cutoff:3.500A) Processing helix chain 'C' and resid 255 through 264 Processing helix chain 'C' and resid 269 through 282 Processing helix chain 'C' and resid 288 through 301 removed outlier: 3.511A pdb=" N ALA C 292 " --> pdb=" O THR C 288 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N GLN C 293 " --> pdb=" O LYS C 289 " (cutoff:3.500A) Processing helix chain 'C' and resid 309 through 321 Processing helix chain 'C' and resid 334 through 349 Processing helix chain 'C' and resid 380 through 407 removed outlier: 3.644A pdb=" N ARG C 395 " --> pdb=" O VAL C 391 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N THR C 405 " --> pdb=" O ARG C 401 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N THR C 406 " --> pdb=" O GLU C 402 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLN C 407 " --> pdb=" O ARG C 403 " (cutoff:3.500A) Processing helix chain 'C' and resid 413 through 418 Processing helix chain 'C' and resid 420 through 432 Processing helix chain 'C' and resid 444 through 452 Processing helix chain 'C' and resid 470 through 474 Processing helix chain 'C' and resid 476 through 480 Processing helix chain 'C' and resid 532 through 538 Processing helix chain 'C' and resid 590 through 594 Processing helix chain 'C' and resid 596 through 600 Processing helix chain 'C' and resid 601 through 612 Processing helix chain 'C' and resid 613 through 615 No H-bonds generated for 'chain 'C' and resid 613 through 615' Processing helix chain 'C' and resid 630 through 637 removed outlier: 3.558A pdb=" N ALA C 635 " --> pdb=" O GLU C 631 " (cutoff:3.500A) Processing helix chain 'C' and resid 739 through 744 Processing helix chain 'C' and resid 778 through 782 Processing helix chain 'C' and resid 815 through 826 Processing helix chain 'C' and resid 922 through 926 removed outlier: 3.540A pdb=" N MET C 926 " --> pdb=" O PRO C 923 " (cutoff:3.500A) Processing helix chain 'C' and resid 928 through 943 Processing helix chain 'C' and resid 953 through 957 removed outlier: 3.607A pdb=" N ALA C 957 " --> pdb=" O ASP C 954 " (cutoff:3.500A) Processing helix chain 'C' and resid 981 through 991 removed outlier: 3.627A pdb=" N CYS C 991 " --> pdb=" O GLY C 987 " (cutoff:3.500A) Processing helix chain 'C' and resid 1069 through 1080 Processing helix chain 'C' and resid 1081 through 1091 Processing helix chain 'C' and resid 1095 through 1109 removed outlier: 4.285A pdb=" N VAL C1100 " --> pdb=" O THR C1096 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N LYS C1101 " --> pdb=" O VAL C1097 " (cutoff:3.500A) Processing helix chain 'C' and resid 1118 through 1131 removed outlier: 3.600A pdb=" N LYS C1122 " --> pdb=" O PRO C1118 " (cutoff:3.500A) Processing helix chain 'D' and resid 16 through 24 Processing helix chain 'D' and resid 86 through 90 Processing helix chain 'D' and resid 104 through 107 Processing helix chain 'D' and resid 112 through 119 Processing helix chain 'D' and resid 121 through 130 removed outlier: 4.388A pdb=" N LYS D 127 " --> pdb=" O LYS D 123 " (cutoff:3.500A) Processing helix chain 'D' and resid 140 through 186 removed outlier: 5.485A pdb=" N SER D 149 " --> pdb=" O HIS D 145 " (cutoff:3.500A) removed outlier: 5.864A pdb=" N THR D 150 " --> pdb=" O ASN D 146 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N VAL D 162 " --> pdb=" O GLU D 158 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ALA D 186 " --> pdb=" O ALA D 182 " (cutoff:3.500A) Processing helix chain 'D' and resid 190 through 228 removed outlier: 3.700A pdb=" N ARG D 194 " --> pdb=" O LYS D 190 " (cutoff:3.500A) Processing helix chain 'D' and resid 238 through 246 removed outlier: 4.727A pdb=" N ASP D 246 " --> pdb=" O ARG D 242 " (cutoff:3.500A) Processing helix chain 'D' and resid 248 through 250 No H-bonds generated for 'chain 'D' and resid 248 through 250' Processing helix chain 'D' and resid 257 through 267 Processing helix chain 'D' and resid 269 through 284 removed outlier: 4.299A pdb=" N GLU D 273 " --> pdb=" O ASP D 269 " (cutoff:3.500A) Processing helix chain 'D' and resid 286 through 305 removed outlier: 4.080A pdb=" N VAL D 298 " --> pdb=" O LYS D 294 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N SER D 305 " --> pdb=" O ALA D 301 " (cutoff:3.500A) Processing helix chain 'D' and resid 308 through 311 Processing helix chain 'D' and resid 321 through 325 Processing helix chain 'D' and resid 339 through 361 removed outlier: 4.321A pdb=" N LEU D 343 " --> pdb=" O ASP D 339 " (cutoff:3.500A) Processing helix chain 'D' and resid 363 through 383 Processing helix chain 'D' and resid 402 through 406 Processing helix chain 'D' and resid 411 through 419 removed outlier: 3.584A pdb=" N GLY D 419 " --> pdb=" O GLN D 415 " (cutoff:3.500A) Processing helix chain 'D' and resid 445 through 452 removed outlier: 3.553A pdb=" N GLU D 450 " --> pdb=" O LEU D 446 " (cutoff:3.500A) Processing helix chain 'D' and resid 452 through 463 Processing helix chain 'D' and resid 469 through 479 Processing helix chain 'D' and resid 481 through 492 removed outlier: 4.044A pdb=" N ASP D 485 " --> pdb=" O PRO D 481 " (cutoff:3.500A) Processing helix chain 'D' and resid 505 through 507 No H-bonds generated for 'chain 'D' and resid 505 through 507' Processing helix chain 'D' and resid 525 through 527 No H-bonds generated for 'chain 'D' and resid 525 through 527' Processing helix chain 'D' and resid 528 through 533 Processing helix chain 'D' and resid 548 through 558 Processing helix chain 'D' and resid 578 through 590 removed outlier: 4.100A pdb=" N THR D 583 " --> pdb=" O LEU D 579 " (cutoff:3.500A) Processing helix chain 'D' and resid 614 through 624 Processing helix chain 'D' and resid 643 through 651 Processing helix chain 'D' and resid 668 through 677 removed outlier: 3.592A pdb=" N LEU D 676 " --> pdb=" O MET D 672 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N LEU D 677 " --> pdb=" O PHE D 673 " (cutoff:3.500A) Processing helix chain 'D' and resid 689 through 704 Processing helix chain 'D' and resid 705 through 726 removed outlier: 3.859A pdb=" N ARG D 726 " --> pdb=" O TYR D 722 " (cutoff:3.500A) Processing helix chain 'D' and resid 741 through 762 Processing helix chain 'D' and resid 766 through 793 removed outlier: 3.517A pdb=" N ARG D 770 " --> pdb=" O ASN D 766 " (cutoff:3.500A) Processing helix chain 'D' and resid 797 through 806 removed outlier: 3.579A pdb=" N VAL D 803 " --> pdb=" O ILE D 799 " (cutoff:3.500A) Processing helix chain 'D' and resid 810 through 818 removed outlier: 3.921A pdb=" N THR D 814 " --> pdb=" O ASN D 810 " (cutoff:3.500A) Processing helix chain 'D' and resid 845 through 882 removed outlier: 4.102A pdb=" N HIS D 854 " --> pdb=" O PHE D 850 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N GLY D 855 " --> pdb=" O ILE D 851 " (cutoff:3.500A) Processing helix chain 'D' and resid 945 through 956 Processing helix chain 'D' and resid 976 through 980 Processing helix chain 'D' and resid 994 through 1005 Processing helix chain 'D' and resid 1006 through 1008 No H-bonds generated for 'chain 'D' and resid 1006 through 1008' Processing helix chain 'D' and resid 1027 through 1037 Processing helix chain 'D' and resid 1117 through 1145 removed outlier: 3.757A pdb=" N VAL D1121 " --> pdb=" O ASP D1117 " (cutoff:3.500A) Proline residue: D1127 - end of helix removed outlier: 3.667A pdb=" N VAL D1130 " --> pdb=" O GLY D1126 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N VAL D1141 " --> pdb=" O GLU D1137 " (cutoff:3.500A) Processing helix chain 'D' and resid 1150 through 1162 removed outlier: 4.529A pdb=" N ILE D1154 " --> pdb=" O HIS D1150 " (cutoff:3.500A) Processing helix chain 'D' and resid 1183 through 1194 Processing helix chain 'D' and resid 1209 through 1216 Processing helix chain 'D' and resid 1219 through 1224 Processing helix chain 'D' and resid 1228 through 1240 removed outlier: 3.661A pdb=" N ASP D1235 " --> pdb=" O ARG D1231 " (cutoff:3.500A) Processing helix chain 'D' and resid 1247 through 1254 removed outlier: 4.184A pdb=" N ASN D1251 " --> pdb=" O GLY D1247 " (cutoff:3.500A) Processing helix chain 'D' and resid 1264 through 1269 Processing helix chain 'D' and resid 1275 through 1282 Processing helix chain 'E' and resid 33 through 37 removed outlier: 3.595A pdb=" N THR E 36 " --> pdb=" O LEU E 33 " (cutoff:3.500A) Processing helix chain 'E' and resid 39 through 44 Processing helix chain 'E' and resid 49 through 71 removed outlier: 3.512A pdb=" N LEU E 53 " --> pdb=" O SER E 49 " (cutoff:3.500A) Processing helix chain 'E' and resid 90 through 101 Processing helix chain 'F' and resid 210 through 223 removed outlier: 4.249A pdb=" N GLU F 220 " --> pdb=" O ARG F 216 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N LEU F 221 " --> pdb=" O LYS F 217 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N THR F 222 " --> pdb=" O ASP F 218 " (cutoff:3.500A) Processing helix chain 'F' and resid 226 through 236 Processing helix chain 'F' and resid 242 through 267 Processing helix chain 'F' and resid 274 through 308 removed outlier: 4.185A pdb=" N ASP F 289 " --> pdb=" O CYS F 285 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ARG F 290 " --> pdb=" O ARG F 286 " (cutoff:3.500A) removed outlier: 4.976A pdb=" N ARG F 301 " --> pdb=" O GLU F 297 " (cutoff:3.500A) removed outlier: 4.833A pdb=" N LEU F 302 " --> pdb=" O ALA F 298 " (cutoff:3.500A) Processing helix chain 'F' and resid 309 through 311 No H-bonds generated for 'chain 'F' and resid 309 through 311' Processing helix chain 'F' and resid 316 through 334 removed outlier: 3.626A pdb=" N LEU F 320 " --> pdb=" O ALA F 316 " (cutoff:3.500A) Processing helix chain 'F' and resid 342 through 362 removed outlier: 3.820A pdb=" N TYR F 346 " --> pdb=" O LYS F 342 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N TRP F 349 " --> pdb=" O THR F 345 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N TRP F 350 " --> pdb=" O TYR F 346 " (cutoff:3.500A) Processing helix chain 'F' and resid 369 through 391 Processing helix chain 'F' and resid 395 through 403 Processing helix chain 'F' and resid 406 through 417 Processing helix chain 'F' and resid 434 through 437 Processing helix chain 'F' and resid 448 through 466 Processing helix chain 'F' and resid 468 through 479 Processing helix chain 'F' and resid 488 through 496 Processing helix chain 'F' and resid 499 through 515 Processing helix chain 'F' and resid 516 through 525 removed outlier: 5.885A pdb=" N VAL F 522 " --> pdb=" O SER F 518 " (cutoff:3.500A) removed outlier: 5.216A pdb=" N LEU F 523 " --> pdb=" O ARG F 519 " (cutoff:3.500A) Processing helix chain 'J' and resid 80 through 87 Processing helix chain 'J' and resid 90 through 110 Processing helix chain 'M' and resid 52 through 57 Processing helix chain 'M' and resid 63 through 74 Processing helix chain 'M' and resid 84 through 99 Processing helix chain 'M' and resid 100 through 118 Processing helix chain 'M' and resid 121 through 143 Processing helix chain 'M' and resid 146 through 158 removed outlier: 3.742A pdb=" N GLU M 156 " --> pdb=" O THR M 152 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 8 through 13 removed outlier: 6.075A pdb=" N ASP A 190 " --> pdb=" O PRO A 25 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 93 through 100 removed outlier: 7.934A pdb=" N GLU A 135 " --> pdb=" O ILE A 56 " (cutoff:3.500A) removed outlier: 4.892A pdb=" N ILE A 56 " --> pdb=" O GLU A 135 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N GLU A 137 " --> pdb=" O ILE A 54 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N ILE A 54 " --> pdb=" O GLU A 137 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N VAL A 139 " --> pdb=" O THR A 52 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 93 through 100 Processing sheet with id=AA4, first strand: chain 'A' and resid 85 through 86 Processing sheet with id=AA5, first strand: chain 'A' and resid 103 through 106 Processing sheet with id=AA6, first strand: chain 'B' and resid 8 through 13 removed outlier: 3.573A pdb=" N SER B 19 " --> pdb=" O VAL B 196 " (cutoff:3.500A) removed outlier: 5.911A pdb=" N ASP B 190 " --> pdb=" O PRO B 25 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N ILE B 193 " --> pdb=" O TYR B 176 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N TYR B 176 " --> pdb=" O ILE B 193 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N ASP B 195 " --> pdb=" O VAL B 174 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N VAL B 174 " --> pdb=" O ASP B 195 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N GLU B 197 " --> pdb=" O LEU B 172 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 93 through 94 Processing sheet with id=AA8, first strand: chain 'B' and resid 93 through 94 removed outlier: 7.652A pdb=" N GLU B 135 " --> pdb=" O ILE B 56 " (cutoff:3.500A) removed outlier: 4.968A pdb=" N ILE B 56 " --> pdb=" O GLU B 135 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N GLU B 137 " --> pdb=" O ILE B 54 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N ILE B 54 " --> pdb=" O GLU B 137 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N VAL B 139 " --> pdb=" O THR B 52 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 85 through 86 Processing sheet with id=AB1, first strand: chain 'B' and resid 103 through 106 Processing sheet with id=AB2, first strand: chain 'B' and resid 146 through 147 Processing sheet with id=AB3, first strand: chain 'C' and resid 39 through 40 removed outlier: 6.206A pdb=" N VAL C 39 " --> pdb=" O SER C 973 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'C' and resid 96 through 97 removed outlier: 6.966A pdb=" N PHE C 134 " --> pdb=" O PRO C 110 " (cutoff:3.500A) removed outlier: 4.892A pdb=" N PHE C 112 " --> pdb=" O PRO C 132 " (cutoff:3.500A) removed outlier: 6.070A pdb=" N ALA C 131 " --> pdb=" O ASP C 156 " (cutoff:3.500A) removed outlier: 4.782A pdb=" N ASP C 156 " --> pdb=" O ALA C 131 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N LEU C 133 " --> pdb=" O MET C 154 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 166 through 168 Processing sheet with id=AB6, first strand: chain 'C' and resid 378 through 379 Processing sheet with id=AB7, first strand: chain 'C' and resid 184 through 189 Processing sheet with id=AB8, first strand: chain 'C' and resid 215 through 216 Processing sheet with id=AB9, first strand: chain 'C' and resid 354 through 355 Processing sheet with id=AC1, first strand: chain 'C' and resid 505 through 506 removed outlier: 5.130A pdb=" N GLU C 527 " --> pdb=" O LYS C 518 " (cutoff:3.500A) removed outlier: 7.162A pdb=" N VAL C 520 " --> pdb=" O SER C 525 " (cutoff:3.500A) removed outlier: 5.985A pdb=" N SER C 525 " --> pdb=" O VAL C 520 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 505 through 506 Processing sheet with id=AC3, first strand: chain 'C' and resid 558 through 562 Processing sheet with id=AC4, first strand: chain 'C' and resid 642 through 644 removed outlier: 6.756A pdb=" N VAL C 642 " --> pdb=" O ILE C 702 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N GLN C 700 " --> pdb=" O ALA C 644 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 667 through 668 removed outlier: 6.840A pdb=" N THR C 659 " --> pdb=" O GLU C 651 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 708 through 709 Processing sheet with id=AC7, first strand: chain 'C' and resid 1007 through 1008 removed outlier: 6.896A pdb=" N ILE C 735 " --> pdb=" O GLY C 896 " (cutoff:3.500A) removed outlier: 6.045A pdb=" N ILE C 898 " --> pdb=" O ILE C 735 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N LEU C 737 " --> pdb=" O ILE C 898 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ILE C 736 " --> pdb=" O ILE C 916 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 765 through 766 removed outlier: 3.623A pdb=" N GLY C 765 " --> pdb=" O THR C 762 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N SER C 749 " --> pdb=" O LYS C 876 " (cutoff:3.500A) removed outlier: 4.864A pdb=" N LYS C 876 " --> pdb=" O SER C 749 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N HIS C 751 " --> pdb=" O ALA C 874 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N ALA C 874 " --> pdb=" O HIS C 751 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N GLU C 753 " --> pdb=" O TYR C 872 " (cutoff:3.500A) removed outlier: 4.692A pdb=" N TYR C 872 " --> pdb=" O GLU C 753 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N HIS C 755 " --> pdb=" O ARG C 870 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N ARG C 870 " --> pdb=" O HIS C 755 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N ILE C 757 " --> pdb=" O LEU C 868 " (cutoff:3.500A) removed outlier: 4.834A pdb=" N LEU C 868 " --> pdb=" O ILE C 757 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N ALA C 759 " --> pdb=" O ASN C 866 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N GLY C 849 " --> pdb=" O TYR C 872 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N ALA C 874 " --> pdb=" O VAL C 847 " (cutoff:3.500A) removed outlier: 4.937A pdb=" N VAL C 847 " --> pdb=" O ALA C 874 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 768 through 769 Processing sheet with id=AD1, first strand: chain 'C' and resid 801 through 803 removed outlier: 6.582A pdb=" N LEU C 837 " --> pdb=" O LEU C 802 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 1042 through 1044 removed outlier: 6.532A pdb=" N CYS D 441 " --> pdb=" O MET D 515 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N VAL D 517 " --> pdb=" O CYS D 441 " (cutoff:3.500A) removed outlier: 5.263A pdb=" N LEU D 443 " --> pdb=" O VAL D 517 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 1042 through 1044 removed outlier: 7.605A pdb=" N ILE D 522 " --> pdb=" O ARG D 427 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N VAL D 429 " --> pdb=" O ILE D 522 " (cutoff:3.500A) removed outlier: 7.369A pdb=" N LEU D 524 " --> pdb=" O VAL D 429 " (cutoff:3.500A) removed outlier: 6.142A pdb=" N VAL D 431 " --> pdb=" O LEU D 524 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 1066 through 1068 removed outlier: 3.942A pdb=" N GLN C1066 " --> pdb=" O VAL D 422 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LYS D 420 " --> pdb=" O PHE C1068 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 1133 through 1138 Processing sheet with id=AD6, first strand: chain 'D' and resid 93 through 102 removed outlier: 10.195A pdb=" N LEU D 97 " --> pdb=" O PRO D 318 " (cutoff:3.500A) removed outlier: 10.697A pdb=" N ALA D 99 " --> pdb=" O ALA D 316 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N ALA D 316 " --> pdb=" O ALA D 99 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'D' and resid 233 through 236 removed outlier: 4.054A pdb=" N GLN D 233 " --> pdb=" O ILE D 136 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N THR D 253 " --> pdb=" O THR D 137 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'F' and resid 421 through 422 removed outlier: 6.219A pdb=" N PHE D 335 " --> pdb=" O ILE F 421 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N GLN D 329 " --> pdb=" O SER J 9 " (cutoff:3.500A) removed outlier: 6.046A pdb=" N GLU F 440 " --> pdb=" O GLY J 8 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'D' and resid 611 through 612 Processing sheet with id=AE1, first strand: chain 'D' and resid 886 through 888 Processing sheet with id=AE2, first strand: chain 'D' and resid 897 through 899 removed outlier: 3.636A pdb=" N VAL D 899 " --> pdb=" O VAL D 960 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N VAL D 960 " --> pdb=" O VAL D 899 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'D' and resid 929 through 930 removed outlier: 7.163A pdb=" N ALA D 929 " --> pdb=" O ILE D 937 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'D' and resid 1053 through 1054 removed outlier: 3.964A pdb=" N ILE D1080 " --> pdb=" O TYR D1062 " (cutoff:3.500A) removed outlier: 5.496A pdb=" N ILE D1064 " --> pdb=" O ASP D1078 " (cutoff:3.500A) removed outlier: 4.831A pdb=" N ASP D1078 " --> pdb=" O ILE D1064 " (cutoff:3.500A) removed outlier: 7.424A pdb=" N ILE D1066 " --> pdb=" O VAL D1076 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N VAL D1076 " --> pdb=" O ILE D1066 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'D' and resid 1181 through 1182 removed outlier: 6.540A pdb=" N ALA D1202 " --> pdb=" O ILE D1168 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'D' and resid 1271 through 1274 Processing sheet with id=AE7, first strand: chain 'J' and resid 39 through 45 Processing sheet with id=AE8, first strand: chain 'M' and resid 45 through 49 removed outlier: 5.913A pdb=" N TYR M 34 " --> pdb=" O ILE M 22 " (cutoff:3.500A) removed outlier: 4.660A pdb=" N ILE M 22 " --> pdb=" O TYR M 34 " (cutoff:3.500A) removed outlier: 7.100A pdb=" N VAL M 36 " --> pdb=" O GLU M 20 " (cutoff:3.500A) 1234 hydrogen bonds defined for protein. 3504 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 145 hydrogen bonds 290 hydrogen bond angles 0 basepair planarities 56 basepair parallelities 101 stacking parallelities Total time for adding SS restraints: 8.23 Time building geometry restraints manager: 3.48 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 8051 1.33 - 1.45: 5583 1.45 - 1.57: 16486 1.57 - 1.69: 247 1.69 - 1.81: 175 Bond restraints: 30542 Sorted by residual: bond pdb=" C ARG C 421 " pdb=" N PRO C 422 " ideal model delta sigma weight residual 1.336 1.396 -0.061 1.23e-02 6.61e+03 2.42e+01 bond pdb=" CA ILE C 773 " pdb=" C ILE C 773 " ideal model delta sigma weight residual 1.524 1.480 0.045 1.05e-02 9.07e+03 1.80e+01 bond pdb=" C VAL C 922 " pdb=" N PRO C 923 " ideal model delta sigma weight residual 1.336 1.378 -0.043 1.23e-02 6.61e+03 1.21e+01 bond pdb=" CA ALA A 222 " pdb=" C ALA A 222 " ideal model delta sigma weight residual 1.524 1.481 0.043 1.27e-02 6.20e+03 1.15e+01 bond pdb=" CA ALA C 634 " pdb=" C ALA C 634 " ideal model delta sigma weight residual 1.523 1.478 0.045 1.35e-02 5.49e+03 1.10e+01 ... (remaining 30537 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.63: 41432 3.63 - 7.25: 429 7.25 - 10.88: 36 10.88 - 14.50: 6 14.50 - 18.13: 3 Bond angle restraints: 41906 Sorted by residual: angle pdb=" C ARG C 282 " pdb=" N PRO C 283 " pdb=" CA PRO C 283 " ideal model delta sigma weight residual 119.99 103.99 16.00 1.08e+00 8.57e-01 2.20e+02 angle pdb=" N LEU A 225 " pdb=" CA LEU A 225 " pdb=" C LEU A 225 " ideal model delta sigma weight residual 113.37 99.17 14.20 1.38e+00 5.25e-01 1.06e+02 angle pdb=" C ILE C 773 " pdb=" N PRO C 774 " pdb=" CA PRO C 774 " ideal model delta sigma weight residual 119.84 129.19 -9.35 1.25e+00 6.40e-01 5.59e+01 angle pdb=" C ARG D 834 " pdb=" N PRO D 835 " pdb=" CA PRO D 835 " ideal model delta sigma weight residual 127.00 142.39 -15.39 2.40e+00 1.74e-01 4.11e+01 angle pdb=" C ARG D 834 " pdb=" N PRO D 835 " pdb=" CD PRO D 835 " ideal model delta sigma weight residual 120.60 106.71 13.89 2.20e+00 2.07e-01 3.98e+01 ... (remaining 41901 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.43: 17556 35.43 - 70.86: 755 70.86 - 106.29: 11 106.29 - 141.72: 0 141.72 - 177.15: 5 Dihedral angle restraints: 18327 sinusoidal: 8279 harmonic: 10048 Sorted by residual: dihedral pdb=" N GLU A 224 " pdb=" C GLU A 224 " pdb=" CA GLU A 224 " pdb=" CB GLU A 224 " ideal model delta harmonic sigma weight residual 122.80 138.78 -15.98 0 2.50e+00 1.60e-01 4.08e+01 dihedral pdb=" C GLU A 224 " pdb=" N GLU A 224 " pdb=" CA GLU A 224 " pdb=" CB GLU A 224 " ideal model delta harmonic sigma weight residual -122.60 -137.99 15.39 0 2.50e+00 1.60e-01 3.79e+01 dihedral pdb=" CA VAL D 4 " pdb=" C VAL D 4 " pdb=" N ASN D 5 " pdb=" CA ASN D 5 " ideal model delta harmonic sigma weight residual 180.00 151.63 28.37 0 5.00e+00 4.00e-02 3.22e+01 ... (remaining 18324 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.150: 4704 0.150 - 0.300: 65 0.300 - 0.450: 3 0.450 - 0.600: 1 0.600 - 0.750: 2 Chirality restraints: 4775 Sorted by residual: chirality pdb=" CA GLU A 224 " pdb=" N GLU A 224 " pdb=" C GLU A 224 " pdb=" CB GLU A 224 " both_signs ideal model delta sigma weight residual False 2.51 1.76 0.75 2.00e-01 2.50e+01 1.40e+01 chirality pdb=" CG LEU A 221 " pdb=" CB LEU A 221 " pdb=" CD1 LEU A 221 " pdb=" CD2 LEU A 221 " both_signs ideal model delta sigma weight residual False -2.59 -1.92 -0.67 2.00e-01 2.50e+01 1.11e+01 chirality pdb=" CA ARG A 223 " pdb=" N ARG A 223 " pdb=" C ARG A 223 " pdb=" CB ARG A 223 " both_signs ideal model delta sigma weight residual False 2.51 2.00 0.51 2.00e-01 2.50e+01 6.51e+00 ... (remaining 4772 not shown) Planarity restraints: 5070 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG M 75 " 0.023 2.00e-02 2.50e+03 4.75e-02 2.26e+01 pdb=" C ARG M 75 " -0.082 2.00e-02 2.50e+03 pdb=" O ARG M 75 " 0.032 2.00e-02 2.50e+03 pdb=" N ALA M 76 " 0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR E 56 " -0.031 2.00e-02 2.50e+03 2.24e-02 1.00e+01 pdb=" CG TYR E 56 " 0.053 2.00e-02 2.50e+03 pdb=" CD1 TYR E 56 " -0.012 2.00e-02 2.50e+03 pdb=" CD2 TYR E 56 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR E 56 " 0.005 2.00e-02 2.50e+03 pdb=" CE2 TYR E 56 " -0.004 2.00e-02 2.50e+03 pdb=" CZ TYR E 56 " -0.004 2.00e-02 2.50e+03 pdb=" OH TYR E 56 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DG O 21 " 0.039 2.00e-02 2.50e+03 1.65e-02 8.19e+00 pdb=" N9 DG O 21 " -0.031 2.00e-02 2.50e+03 pdb=" C8 DG O 21 " -0.001 2.00e-02 2.50e+03 pdb=" N7 DG O 21 " -0.012 2.00e-02 2.50e+03 pdb=" C5 DG O 21 " -0.006 2.00e-02 2.50e+03 pdb=" C6 DG O 21 " 0.015 2.00e-02 2.50e+03 pdb=" O6 DG O 21 " 0.013 2.00e-02 2.50e+03 pdb=" N1 DG O 21 " 0.005 2.00e-02 2.50e+03 pdb=" C2 DG O 21 " -0.013 2.00e-02 2.50e+03 pdb=" N2 DG O 21 " -0.001 2.00e-02 2.50e+03 pdb=" N3 DG O 21 " -0.004 2.00e-02 2.50e+03 pdb=" C4 DG O 21 " -0.004 2.00e-02 2.50e+03 ... (remaining 5067 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.65: 571 2.65 - 3.21: 26564 3.21 - 3.77: 50049 3.77 - 4.34: 63859 4.34 - 4.90: 99898 Nonbonded interactions: 240941 Sorted by model distance: nonbonded pdb=" NH2 ARG F 502 " pdb=" OP2 DT O 23 " model vdw 2.082 3.120 nonbonded pdb=" OD1 ASP D 537 " pdb="MG MG D2002 " model vdw 2.099 2.170 nonbonded pdb=" O GLY D 408 " pdb=" NH1 ARG D 414 " model vdw 2.120 3.120 nonbonded pdb=" OD1 ASP D 535 " pdb="MG MG D2002 " model vdw 2.126 2.170 nonbonded pdb=" OD2 ASP D 537 " pdb="MG MG D2002 " model vdw 2.129 2.170 ... (remaining 240936 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 2 through 99 or (resid 100 and (name N or name CA or name \ C or name O or name CB )) or resid 101 through 129 or (resid 130 and (name N or \ name CA or name C or name O or name CB )) or resid 131 through 134 or (resid 135 \ and (name N or name CA or name C or name O or name CB )) or resid 136 through 1 \ 52 or (resid 153 through 154 and (name N or name CA or name C or name O or name \ CB )) or resid 155 through 157 or (resid 158 and (name N or name CA or name C or \ name O or name CB )) or resid 159 through 160 or (resid 161 and (name N or name \ CA or name C or name O or name CB )) or resid 162 through 183 or (resid 184 and \ (name N or name CA or name C or name O or name CB )) or resid 185 or (resid 186 \ and (name N or name CA or name C or name O or name CB )) or resid 187 through 2 \ 23 or (resid 224 and (name N or name CA or name C or name O or name CB )) or res \ id 225 through 226)) selection = (chain 'B' and resid 2 through 226) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.040 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.470 Check model and map are aligned: 0.090 Set scattering table: 0.080 Process input model: 36.990 Find NCS groups from input model: 0.350 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.450 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.540 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8651 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.224 30549 Z= 0.336 Angle : 1.064 32.885 41912 Z= 0.609 Chirality : 0.058 0.750 4775 Planarity : 0.007 0.060 5070 Dihedral : 16.003 177.146 11863 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.51 % Favored : 93.38 % Rotamer: Outliers : 0.65 % Allowed : 5.01 % Favored : 94.34 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.18 (0.12), residues: 3488 helix: -1.64 (0.11), residues: 1366 sheet: -2.12 (0.25), residues: 349 loop : -2.50 (0.13), residues: 1773 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG D 556 TYR 0.053 0.003 TYR E 56 PHE 0.042 0.003 PHE D 6 TRP 0.035 0.004 TRP C 70 HIS 0.014 0.003 HIS C 751 Details of bonding type rmsd covalent geometry : bond 0.00671 (30542) covalent geometry : angle 1.04408 (41906) hydrogen bonds : bond 0.16934 ( 1363) hydrogen bonds : angle 7.14610 ( 3794) metal coordination : bond 0.14718 ( 7) metal coordination : angle 17.26583 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6976 Ramachandran restraints generated. 3488 Oldfield, 0 Emsley, 3488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6976 Ramachandran restraints generated. 3488 Oldfield, 0 Emsley, 3488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 2960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 219 time to evaluate : 1.261 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 MET cc_start: 0.8782 (ptp) cc_final: 0.8582 (pmm) REVERT: B 191 LYS cc_start: 0.9295 (ttpt) cc_final: 0.8709 (tttp) REVERT: B 226 ASN cc_start: 0.8834 (t160) cc_final: 0.8563 (t0) REVERT: C 202 VAL cc_start: 0.8855 (OUTLIER) cc_final: 0.8472 (m) REVERT: C 355 MET cc_start: 0.8995 (tmm) cc_final: 0.8686 (tmm) REVERT: C 396 MET cc_start: 0.9463 (tmt) cc_final: 0.8889 (tmm) REVERT: C 607 MET cc_start: 0.8781 (mtt) cc_final: 0.8495 (mtm) REVERT: C 611 MET cc_start: 0.9310 (mtm) cc_final: 0.8940 (ptp) REVERT: C 630 MET cc_start: 0.8955 (mmm) cc_final: 0.8667 (mmm) REVERT: C 733 ASP cc_start: 0.8636 (m-30) cc_final: 0.8399 (p0) REVERT: C 1038 ASP cc_start: 0.9185 (m-30) cc_final: 0.8738 (p0) REVERT: C 1088 LEU cc_start: 0.9545 (mt) cc_final: 0.9286 (pp) REVERT: C 1119 GLU cc_start: 0.8715 (tp30) cc_final: 0.8385 (tp30) REVERT: D 114 LEU cc_start: 0.9559 (mt) cc_final: 0.9176 (mt) REVERT: D 256 MET cc_start: 0.8351 (ttm) cc_final: 0.7784 (ttm) REVERT: D 373 MET cc_start: 0.8987 (mtp) cc_final: 0.8760 (mtp) REVERT: D 491 ILE cc_start: 0.9579 (mt) cc_final: 0.9363 (pt) REVERT: D 541 MET cc_start: 0.8606 (mtp) cc_final: 0.8069 (mtp) REVERT: D 1112 MET cc_start: 0.7305 (mmm) cc_final: 0.6858 (mmm) REVERT: E 41 ASP cc_start: 0.8792 (m-30) cc_final: 0.8444 (m-30) REVERT: E 42 GLU cc_start: 0.9539 (mt-10) cc_final: 0.8750 (tp30) REVERT: E 66 ASP cc_start: 0.9148 (m-30) cc_final: 0.8946 (t0) REVERT: E 105 GLU cc_start: 0.8676 (pt0) cc_final: 0.8440 (pt0) outliers start: 19 outliers final: 7 residues processed: 237 average time/residue: 0.2284 time to fit residues: 84.0437 Evaluate side-chains 130 residues out of total 2960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 122 time to evaluate : 0.912 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain C residue 202 VAL Chi-restraints excluded: chain C residue 282 ARG Chi-restraints excluded: chain C residue 773 ILE Chi-restraints excluded: chain C residue 839 VAL Chi-restraints excluded: chain C residue 1131 LEU Chi-restraints excluded: chain C residue 1137 VAL Chi-restraints excluded: chain D residue 578 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 358 random chunks: chunk 197 optimal weight: 8.9990 chunk 215 optimal weight: 7.9990 chunk 20 optimal weight: 6.9990 chunk 132 optimal weight: 5.9990 chunk 261 optimal weight: 20.0000 chunk 248 optimal weight: 9.9990 chunk 207 optimal weight: 8.9990 chunk 155 optimal weight: 9.9990 chunk 244 optimal weight: 5.9990 chunk 183 optimal weight: 2.9990 chunk 298 optimal weight: 7.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 61 HIS B 124 HIS B 151 GLN B 185 GLN B 226 ASN C 81 ASN C 141 ASN C 298 ASN ** C 419 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 476 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 479 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 662 HIS ** C 718 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 729 HIS C 875 GLN C 920 HIS D 22 GLN D 239 ASN D 307 ASN ** D 494 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 564 ASN D 687 GLN D 693 GLN D 771 ASN D 797 ASN ** D1110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1139 GLN D1145 GLN D1190 ASN E 65 ASN E 69 ASN F 516 HIS M 13 HIS M 14 HIS ** M 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 102 ASN Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.035632 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2651 r_free = 0.2651 target = 0.026213 restraints weight = 257401.209| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.2685 r_free = 0.2685 target = 0.027027 restraints weight = 141183.439| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2709 r_free = 0.2709 target = 0.027592 restraints weight = 94677.842| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.2725 r_free = 0.2725 target = 0.027981 restraints weight = 71755.392| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2735 r_free = 0.2735 target = 0.028221 restraints weight = 59408.793| |-----------------------------------------------------------------------------| r_work (final): 0.2714 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2714 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2714 r_free = 0.2714 target_work(ls_wunit_k1) = 0.028 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2713 r_free = 0.2713 target_work(ls_wunit_k1) = 0.028 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2713 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8700 moved from start: 0.1703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.108 30549 Z= 0.285 Angle : 0.739 11.554 41912 Z= 0.392 Chirality : 0.044 0.157 4775 Planarity : 0.006 0.061 5070 Dihedral : 19.496 176.475 5217 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 11.85 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.79 % Favored : 94.15 % Rotamer: Outliers : 1.68 % Allowed : 8.19 % Favored : 90.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.60 (0.14), residues: 3488 helix: 0.09 (0.13), residues: 1407 sheet: -1.73 (0.27), residues: 327 loop : -1.92 (0.14), residues: 1754 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 214 TYR 0.038 0.002 TYR E 56 PHE 0.019 0.002 PHE D 6 TRP 0.021 0.002 TRP C 70 HIS 0.007 0.002 HIS D 889 Details of bonding type rmsd covalent geometry : bond 0.00597 (30542) covalent geometry : angle 0.73667 (41906) hydrogen bonds : bond 0.05194 ( 1363) hydrogen bonds : angle 5.32446 ( 3794) metal coordination : bond 0.01333 ( 7) metal coordination : angle 4.90543 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6976 Ramachandran restraints generated. 3488 Oldfield, 0 Emsley, 3488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6976 Ramachandran restraints generated. 3488 Oldfield, 0 Emsley, 3488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 2960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 129 time to evaluate : 1.131 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 123 MET cc_start: 0.8826 (ttm) cc_final: 0.8389 (tmm) REVERT: B 1 MET cc_start: 0.8430 (tpp) cc_final: 0.7832 (tpp) REVERT: B 191 LYS cc_start: 0.9266 (ttpt) cc_final: 0.8715 (tttp) REVERT: B 226 ASN cc_start: 0.8787 (t0) cc_final: 0.8538 (t0) REVERT: C 103 MET cc_start: 0.9405 (ptp) cc_final: 0.8781 (ppp) REVERT: C 122 CYS cc_start: 0.9300 (m) cc_final: 0.9064 (m) REVERT: C 355 MET cc_start: 0.8895 (tmm) cc_final: 0.8580 (tmm) REVERT: C 393 MET cc_start: 0.9365 (tpp) cc_final: 0.8842 (tpp) REVERT: C 396 MET cc_start: 0.9460 (tmt) cc_final: 0.9128 (tmm) REVERT: C 404 MET cc_start: 0.8517 (ptt) cc_final: 0.8248 (ptp) REVERT: C 586 MET cc_start: 0.8994 (ppp) cc_final: 0.7976 (ppp) REVERT: C 607 MET cc_start: 0.8885 (mtt) cc_final: 0.8513 (mtm) REVERT: C 611 MET cc_start: 0.9166 (mtm) cc_final: 0.8706 (ptp) REVERT: C 630 MET cc_start: 0.8884 (mmm) cc_final: 0.8675 (mmp) REVERT: C 661 MET cc_start: 0.8896 (tpt) cc_final: 0.8602 (tpt) REVERT: C 1038 ASP cc_start: 0.9144 (m-30) cc_final: 0.8779 (p0) REVERT: C 1076 MET cc_start: 0.9150 (mmm) cc_final: 0.8939 (mmm) REVERT: C 1119 GLU cc_start: 0.8723 (tp30) cc_final: 0.8284 (tp30) REVERT: D 114 LEU cc_start: 0.9540 (mt) cc_final: 0.9149 (mt) REVERT: D 143 MET cc_start: 0.9518 (mtp) cc_final: 0.9240 (mtp) REVERT: D 256 MET cc_start: 0.8317 (ttm) cc_final: 0.7901 (ttm) REVERT: D 327 MET cc_start: 0.8653 (tpp) cc_final: 0.8430 (tpt) REVERT: D 491 ILE cc_start: 0.9595 (mt) cc_final: 0.9341 (pt) REVERT: D 516 LEU cc_start: 0.9343 (mt) cc_final: 0.9033 (mt) REVERT: D 706 MET cc_start: 0.9266 (mmm) cc_final: 0.8935 (mmm) REVERT: D 733 MET cc_start: 0.8742 (OUTLIER) cc_final: 0.8466 (tmm) REVERT: D 1112 MET cc_start: 0.7926 (mmm) cc_final: 0.7450 (mmm) REVERT: D 1161 MET cc_start: 0.9136 (mtp) cc_final: 0.8557 (mtp) REVERT: E 41 ASP cc_start: 0.8757 (m-30) cc_final: 0.8541 (m-30) REVERT: E 42 GLU cc_start: 0.9568 (mt-10) cc_final: 0.8792 (tp30) REVERT: E 78 TYR cc_start: 0.8208 (m-10) cc_final: 0.7982 (m-10) REVERT: F 281 MET cc_start: 0.9123 (ptm) cc_final: 0.8869 (ptp) REVERT: J 86 LEU cc_start: 0.9785 (OUTLIER) cc_final: 0.9526 (pp) REVERT: M 11 TYR cc_start: 0.9156 (t80) cc_final: 0.8281 (t80) REVERT: M 55 TYR cc_start: 0.8254 (m-80) cc_final: 0.8018 (m-80) outliers start: 49 outliers final: 15 residues processed: 173 average time/residue: 0.1906 time to fit residues: 54.6122 Evaluate side-chains 132 residues out of total 2960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 115 time to evaluate : 1.163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 70 LYS Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain B residue 125 ILE Chi-restraints excluded: chain C residue 282 ARG Chi-restraints excluded: chain C residue 584 ARG Chi-restraints excluded: chain C residue 626 VAL Chi-restraints excluded: chain C residue 936 LEU Chi-restraints excluded: chain C residue 1089 LEU Chi-restraints excluded: chain C residue 1131 LEU Chi-restraints excluded: chain C residue 1137 VAL Chi-restraints excluded: chain D residue 733 MET Chi-restraints excluded: chain D residue 793 TYR Chi-restraints excluded: chain D residue 1012 MET Chi-restraints excluded: chain J residue 5 VAL Chi-restraints excluded: chain J residue 86 LEU Chi-restraints excluded: chain M residue 147 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 358 random chunks: chunk 1 optimal weight: 0.0980 chunk 129 optimal weight: 3.9990 chunk 59 optimal weight: 4.9990 chunk 168 optimal weight: 5.9990 chunk 351 optimal weight: 4.9990 chunk 345 optimal weight: 10.0000 chunk 46 optimal weight: 8.9990 chunk 78 optimal weight: 10.0000 chunk 182 optimal weight: 0.9980 chunk 314 optimal weight: 7.9990 chunk 328 optimal weight: 20.0000 overall best weight: 3.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 388 GLN ** C 419 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 476 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 718 ASN C1042 HIS C1062 GLN ** D 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 494 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 540 GLN D 854 HIS ** D1110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 88 GLN M 72 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.036119 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2672 r_free = 0.2672 target = 0.026699 restraints weight = 253759.318| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.2708 r_free = 0.2708 target = 0.027551 restraints weight = 137779.734| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.2732 r_free = 0.2732 target = 0.028124 restraints weight = 91429.943| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2746 r_free = 0.2746 target = 0.028483 restraints weight = 69319.617| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.2757 r_free = 0.2757 target = 0.028757 restraints weight = 57778.491| |-----------------------------------------------------------------------------| r_work (final): 0.2737 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2737 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2737 r_free = 0.2737 target_work(ls_wunit_k1) = 0.028 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2737 r_free = 0.2737 target_work(ls_wunit_k1) = 0.028 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2737 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8672 moved from start: 0.2017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 30549 Z= 0.171 Angle : 0.638 11.227 41912 Z= 0.333 Chirality : 0.042 0.162 4775 Planarity : 0.004 0.058 5070 Dihedral : 19.294 177.151 5207 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 9.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.36 % Favored : 94.64 % Rotamer: Outliers : 1.92 % Allowed : 8.64 % Favored : 89.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.99 (0.14), residues: 3488 helix: 0.71 (0.14), residues: 1413 sheet: -1.35 (0.28), residues: 309 loop : -1.71 (0.14), residues: 1766 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 214 TYR 0.032 0.001 TYR E 56 PHE 0.019 0.001 PHE D 6 TRP 0.017 0.001 TRP C 70 HIS 0.004 0.001 HIS D 889 Details of bonding type rmsd covalent geometry : bond 0.00361 (30542) covalent geometry : angle 0.63571 (41906) hydrogen bonds : bond 0.04240 ( 1363) hydrogen bonds : angle 4.87422 ( 3794) metal coordination : bond 0.00584 ( 7) metal coordination : angle 4.07650 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6976 Ramachandran restraints generated. 3488 Oldfield, 0 Emsley, 3488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6976 Ramachandran restraints generated. 3488 Oldfield, 0 Emsley, 3488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 2960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 121 time to evaluate : 1.223 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 123 MET cc_start: 0.8931 (ttm) cc_final: 0.8569 (tmm) REVERT: B 1 MET cc_start: 0.8459 (tpp) cc_final: 0.7878 (tpp) REVERT: B 177 LYS cc_start: 0.8934 (ptmm) cc_final: 0.8518 (ptmm) REVERT: B 226 ASN cc_start: 0.8777 (t0) cc_final: 0.8545 (t0) REVERT: C 103 MET cc_start: 0.9318 (ptp) cc_final: 0.8744 (ppp) REVERT: C 122 CYS cc_start: 0.9150 (m) cc_final: 0.8928 (m) REVERT: C 355 MET cc_start: 0.8823 (tmm) cc_final: 0.8547 (tmm) REVERT: C 393 MET cc_start: 0.9351 (tpp) cc_final: 0.9019 (mmm) REVERT: C 404 MET cc_start: 0.8492 (ptt) cc_final: 0.8117 (ptp) REVERT: C 412 ILE cc_start: 0.9124 (OUTLIER) cc_final: 0.8910 (mm) REVERT: C 561 VAL cc_start: 0.8903 (OUTLIER) cc_final: 0.8660 (p) REVERT: C 586 MET cc_start: 0.9121 (ppp) cc_final: 0.7926 (ppp) REVERT: C 607 MET cc_start: 0.8898 (mtt) cc_final: 0.8505 (mtm) REVERT: C 611 MET cc_start: 0.9201 (mtm) cc_final: 0.8772 (ptp) REVERT: C 630 MET cc_start: 0.8961 (mmm) cc_final: 0.8742 (mmp) REVERT: C 661 MET cc_start: 0.8880 (tpt) cc_final: 0.8606 (tpt) REVERT: C 1038 ASP cc_start: 0.9118 (m-30) cc_final: 0.8784 (p0) REVERT: C 1076 MET cc_start: 0.9269 (mmm) cc_final: 0.8726 (mmm) REVERT: C 1119 GLU cc_start: 0.8697 (tp30) cc_final: 0.8304 (tp30) REVERT: D 114 LEU cc_start: 0.9558 (mt) cc_final: 0.9201 (mt) REVERT: D 143 MET cc_start: 0.9501 (mtp) cc_final: 0.9252 (mtp) REVERT: D 256 MET cc_start: 0.8239 (ttm) cc_final: 0.7824 (ttm) REVERT: D 373 MET cc_start: 0.8756 (mtp) cc_final: 0.8432 (ptp) REVERT: D 733 MET cc_start: 0.8702 (OUTLIER) cc_final: 0.8430 (tmm) REVERT: D 983 MET cc_start: 0.8306 (tpp) cc_final: 0.7967 (tpp) REVERT: D 991 ILE cc_start: 0.8896 (OUTLIER) cc_final: 0.8655 (tp) REVERT: D 1112 MET cc_start: 0.7750 (mmm) cc_final: 0.7263 (mmm) REVERT: E 41 ASP cc_start: 0.8748 (m-30) cc_final: 0.8487 (m-30) REVERT: E 42 GLU cc_start: 0.9574 (mt-10) cc_final: 0.8783 (tp30) REVERT: M 11 TYR cc_start: 0.9150 (t80) cc_final: 0.8261 (t80) REVERT: M 55 TYR cc_start: 0.8124 (m-80) cc_final: 0.7840 (m-80) outliers start: 56 outliers final: 31 residues processed: 172 average time/residue: 0.1865 time to fit residues: 53.4711 Evaluate side-chains 149 residues out of total 2960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 114 time to evaluate : 1.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 95 MET Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain B residue 96 TYR Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain B residue 125 ILE Chi-restraints excluded: chain B residue 147 VAL Chi-restraints excluded: chain B residue 159 ILE Chi-restraints excluded: chain C residue 224 VAL Chi-restraints excluded: chain C residue 282 ARG Chi-restraints excluded: chain C residue 288 THR Chi-restraints excluded: chain C residue 299 LEU Chi-restraints excluded: chain C residue 357 VAL Chi-restraints excluded: chain C residue 412 ILE Chi-restraints excluded: chain C residue 561 VAL Chi-restraints excluded: chain C residue 626 VAL Chi-restraints excluded: chain C residue 839 VAL Chi-restraints excluded: chain C residue 936 LEU Chi-restraints excluded: chain C residue 1131 LEU Chi-restraints excluded: chain C residue 1137 VAL Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 148 LEU Chi-restraints excluded: chain D residue 543 VAL Chi-restraints excluded: chain D residue 733 MET Chi-restraints excluded: chain D residue 793 TYR Chi-restraints excluded: chain D residue 991 ILE Chi-restraints excluded: chain D residue 1012 MET Chi-restraints excluded: chain F residue 328 LEU Chi-restraints excluded: chain F residue 460 LEU Chi-restraints excluded: chain J residue 5 VAL Chi-restraints excluded: chain M residue 25 ARG Chi-restraints excluded: chain M residue 27 ILE Chi-restraints excluded: chain M residue 67 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 358 random chunks: chunk 160 optimal weight: 6.9990 chunk 265 optimal weight: 9.9990 chunk 193 optimal weight: 6.9990 chunk 87 optimal weight: 10.0000 chunk 84 optimal weight: 2.9990 chunk 154 optimal weight: 8.9990 chunk 274 optimal weight: 8.9990 chunk 85 optimal weight: 1.9990 chunk 99 optimal weight: 9.9990 chunk 261 optimal weight: 4.9990 chunk 336 optimal weight: 10.0000 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 419 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 476 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 941 HIS ** D 494 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 540 GLN ** D1110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.035571 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2649 r_free = 0.2649 target = 0.026204 restraints weight = 255709.651| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2684 r_free = 0.2684 target = 0.027021 restraints weight = 141221.096| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.2707 r_free = 0.2707 target = 0.027569 restraints weight = 94991.392| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2721 r_free = 0.2721 target = 0.027918 restraints weight = 72672.673| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 48)----------------| | r_work = 0.2733 r_free = 0.2733 target = 0.028192 restraints weight = 60741.616| |-----------------------------------------------------------------------------| r_work (final): 0.2710 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2711 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2711 r_free = 0.2711 target_work(ls_wunit_k1) = 0.028 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2711 r_free = 0.2711 target_work(ls_wunit_k1) = 0.028 | | occupancies: max = 1.00 min = 0.07 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.2711 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8700 moved from start: 0.2339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.083 30549 Z= 0.232 Angle : 0.666 10.084 41912 Z= 0.346 Chirality : 0.042 0.234 4775 Planarity : 0.005 0.058 5070 Dihedral : 19.199 176.436 5207 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 11.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.85 % Favored : 94.15 % Rotamer: Outliers : 2.13 % Allowed : 9.22 % Favored : 88.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.76 (0.14), residues: 3488 helix: 0.95 (0.14), residues: 1417 sheet: -1.39 (0.27), residues: 333 loop : -1.59 (0.15), residues: 1738 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 166 TYR 0.032 0.002 TYR E 56 PHE 0.017 0.002 PHE D 6 TRP 0.016 0.002 TRP C 70 HIS 0.005 0.001 HIS D 889 Details of bonding type rmsd covalent geometry : bond 0.00489 (30542) covalent geometry : angle 0.66456 (41906) hydrogen bonds : bond 0.04563 ( 1363) hydrogen bonds : angle 4.82707 ( 3794) metal coordination : bond 0.00886 ( 7) metal coordination : angle 3.93891 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6976 Ramachandran restraints generated. 3488 Oldfield, 0 Emsley, 3488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6976 Ramachandran restraints generated. 3488 Oldfield, 0 Emsley, 3488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 2960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 112 time to evaluate : 1.186 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 1 MET cc_start: 0.8551 (tpp) cc_final: 0.7916 (tpp) REVERT: B 70 LYS cc_start: 0.9394 (ttpt) cc_final: 0.9042 (ptpp) REVERT: B 173 LYS cc_start: 0.9085 (tptp) cc_final: 0.8760 (tptp) REVERT: B 177 LYS cc_start: 0.8928 (ptmm) cc_final: 0.8339 (ptmm) REVERT: B 191 LYS cc_start: 0.9224 (ttpt) cc_final: 0.8968 (tptt) REVERT: B 226 ASN cc_start: 0.8730 (t0) cc_final: 0.8526 (t0) REVERT: C 122 CYS cc_start: 0.9139 (m) cc_final: 0.8924 (m) REVERT: C 355 MET cc_start: 0.8795 (tmm) cc_final: 0.8533 (tmm) REVERT: C 393 MET cc_start: 0.9430 (tpp) cc_final: 0.9186 (mmm) REVERT: C 412 ILE cc_start: 0.9224 (OUTLIER) cc_final: 0.8976 (mm) REVERT: C 586 MET cc_start: 0.9261 (ppp) cc_final: 0.8120 (ppp) REVERT: C 607 MET cc_start: 0.8911 (mtt) cc_final: 0.8537 (mtm) REVERT: C 611 MET cc_start: 0.9219 (mtm) cc_final: 0.8758 (ptp) REVERT: C 630 MET cc_start: 0.9004 (mmm) cc_final: 0.8785 (mmp) REVERT: C 661 MET cc_start: 0.8945 (tpt) cc_final: 0.8590 (tpt) REVERT: C 784 LEU cc_start: 0.9409 (OUTLIER) cc_final: 0.9055 (pp) REVERT: C 907 LEU cc_start: 0.9358 (OUTLIER) cc_final: 0.9118 (tm) REVERT: C 1038 ASP cc_start: 0.9025 (m-30) cc_final: 0.8784 (p0) REVERT: C 1051 MET cc_start: 0.9092 (tpt) cc_final: 0.8838 (mmm) REVERT: C 1076 MET cc_start: 0.9382 (mmm) cc_final: 0.8866 (mmm) REVERT: D 143 MET cc_start: 0.9502 (mtp) cc_final: 0.9243 (mtp) REVERT: D 155 MET cc_start: 0.9191 (tmm) cc_final: 0.8915 (tpt) REVERT: D 256 MET cc_start: 0.8167 (ttm) cc_final: 0.7312 (mtp) REVERT: D 327 MET cc_start: 0.8826 (tpt) cc_final: 0.8548 (tpt) REVERT: D 373 MET cc_start: 0.8780 (mtp) cc_final: 0.8454 (ptp) REVERT: D 516 LEU cc_start: 0.9459 (mt) cc_final: 0.9112 (pt) REVERT: D 581 MET cc_start: 0.8940 (pmm) cc_final: 0.8725 (pmm) REVERT: D 706 MET cc_start: 0.9245 (mmm) cc_final: 0.8927 (mmm) REVERT: D 733 MET cc_start: 0.8726 (OUTLIER) cc_final: 0.8505 (tmm) REVERT: D 983 MET cc_start: 0.8308 (tpp) cc_final: 0.7859 (tpp) REVERT: D 1112 MET cc_start: 0.7776 (mmm) cc_final: 0.7498 (mmm) REVERT: E 41 ASP cc_start: 0.8779 (m-30) cc_final: 0.8547 (m-30) REVERT: E 42 GLU cc_start: 0.9572 (mt-10) cc_final: 0.8798 (tp30) REVERT: F 498 VAL cc_start: 0.8679 (OUTLIER) cc_final: 0.8422 (t) REVERT: M 11 TYR cc_start: 0.9126 (t80) cc_final: 0.8282 (t80) outliers start: 62 outliers final: 38 residues processed: 167 average time/residue: 0.1851 time to fit residues: 51.7996 Evaluate side-chains 152 residues out of total 2960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 109 time to evaluate : 1.180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 95 MET Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain B residue 96 TYR Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain B residue 125 ILE Chi-restraints excluded: chain B residue 147 VAL Chi-restraints excluded: chain C residue 224 VAL Chi-restraints excluded: chain C residue 226 ILE Chi-restraints excluded: chain C residue 282 ARG Chi-restraints excluded: chain C residue 288 THR Chi-restraints excluded: chain C residue 299 LEU Chi-restraints excluded: chain C residue 357 VAL Chi-restraints excluded: chain C residue 412 ILE Chi-restraints excluded: chain C residue 584 ARG Chi-restraints excluded: chain C residue 626 VAL Chi-restraints excluded: chain C residue 784 LEU Chi-restraints excluded: chain C residue 868 LEU Chi-restraints excluded: chain C residue 907 LEU Chi-restraints excluded: chain C residue 936 LEU Chi-restraints excluded: chain C residue 1089 LEU Chi-restraints excluded: chain C residue 1131 LEU Chi-restraints excluded: chain C residue 1137 VAL Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 148 LEU Chi-restraints excluded: chain D residue 543 VAL Chi-restraints excluded: chain D residue 559 MET Chi-restraints excluded: chain D residue 729 VAL Chi-restraints excluded: chain D residue 733 MET Chi-restraints excluded: chain D residue 793 TYR Chi-restraints excluded: chain F residue 328 LEU Chi-restraints excluded: chain F residue 460 LEU Chi-restraints excluded: chain F residue 498 VAL Chi-restraints excluded: chain J residue 5 VAL Chi-restraints excluded: chain M residue 25 ARG Chi-restraints excluded: chain M residue 27 ILE Chi-restraints excluded: chain M residue 44 LEU Chi-restraints excluded: chain M residue 67 LEU Chi-restraints excluded: chain M residue 78 HIS Chi-restraints excluded: chain M residue 147 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 358 random chunks: chunk 60 optimal weight: 8.9990 chunk 248 optimal weight: 0.9990 chunk 270 optimal weight: 5.9990 chunk 220 optimal weight: 6.9990 chunk 208 optimal weight: 3.9990 chunk 5 optimal weight: 10.0000 chunk 322 optimal weight: 7.9990 chunk 70 optimal weight: 10.0000 chunk 238 optimal weight: 6.9990 chunk 304 optimal weight: 8.9990 chunk 255 optimal weight: 6.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 419 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 476 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 494 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 70 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.035388 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.2640 r_free = 0.2640 target = 0.026023 restraints weight = 256441.589| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2675 r_free = 0.2675 target = 0.026833 restraints weight = 141745.639| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2699 r_free = 0.2699 target = 0.027394 restraints weight = 95544.310| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2713 r_free = 0.2713 target = 0.027750 restraints weight = 72641.324| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.2726 r_free = 0.2726 target = 0.028032 restraints weight = 60769.241| |-----------------------------------------------------------------------------| r_work (final): 0.2703 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2704 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2704 r_free = 0.2704 target_work(ls_wunit_k1) = 0.028 | | occupancies: max = 1.00 min = 0.07 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2704 r_free = 0.2704 target_work(ls_wunit_k1) = 0.027 | | occupancies: max = 1.00 min = 0.14 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2704 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8707 moved from start: 0.2625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 30549 Z= 0.235 Angle : 0.656 10.159 41912 Z= 0.343 Chirality : 0.042 0.251 4775 Planarity : 0.004 0.059 5070 Dihedral : 19.134 176.357 5207 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 11.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.88 % Favored : 94.12 % Rotamer: Outliers : 2.50 % Allowed : 9.50 % Favored : 88.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.61 (0.14), residues: 3488 helix: 1.09 (0.14), residues: 1423 sheet: -1.12 (0.28), residues: 336 loop : -1.57 (0.15), residues: 1729 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 301 TYR 0.029 0.002 TYR E 56 PHE 0.015 0.002 PHE D 6 TRP 0.014 0.002 TRP C 70 HIS 0.006 0.001 HIS D 889 Details of bonding type rmsd covalent geometry : bond 0.00495 (30542) covalent geometry : angle 0.65407 (41906) hydrogen bonds : bond 0.04440 ( 1363) hydrogen bonds : angle 4.76999 ( 3794) metal coordination : bond 0.00953 ( 7) metal coordination : angle 4.14562 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6976 Ramachandran restraints generated. 3488 Oldfield, 0 Emsley, 3488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6976 Ramachandran restraints generated. 3488 Oldfield, 0 Emsley, 3488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 2960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 114 time to evaluate : 1.161 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 1 MET cc_start: 0.8591 (tpp) cc_final: 0.7846 (tpp) REVERT: B 70 LYS cc_start: 0.9415 (OUTLIER) cc_final: 0.9054 (ptpp) REVERT: B 173 LYS cc_start: 0.9077 (tptp) cc_final: 0.8701 (tptp) REVERT: B 177 LYS cc_start: 0.8933 (ptmm) cc_final: 0.8351 (ptmm) REVERT: B 191 LYS cc_start: 0.9222 (ttpt) cc_final: 0.8982 (tptt) REVERT: C 103 MET cc_start: 0.9259 (ptm) cc_final: 0.8703 (ppp) REVERT: C 159 MET cc_start: 0.9344 (tpp) cc_final: 0.8934 (mmm) REVERT: C 355 MET cc_start: 0.8800 (tmm) cc_final: 0.8488 (tmm) REVERT: C 393 MET cc_start: 0.9427 (tpp) cc_final: 0.9176 (mmm) REVERT: C 404 MET cc_start: 0.8543 (ptp) cc_final: 0.8224 (ptt) REVERT: C 412 ILE cc_start: 0.9276 (OUTLIER) cc_final: 0.9039 (mm) REVERT: C 586 MET cc_start: 0.9295 (ppp) cc_final: 0.8214 (ppp) REVERT: C 607 MET cc_start: 0.8892 (mtt) cc_final: 0.8507 (mtm) REVERT: C 611 MET cc_start: 0.9215 (mtm) cc_final: 0.8780 (mtp) REVERT: C 630 MET cc_start: 0.9000 (mmm) cc_final: 0.8789 (mmp) REVERT: C 661 MET cc_start: 0.8927 (tpt) cc_final: 0.8525 (tpt) REVERT: C 784 LEU cc_start: 0.9390 (OUTLIER) cc_final: 0.9028 (pp) REVERT: C 907 LEU cc_start: 0.9362 (OUTLIER) cc_final: 0.9119 (tm) REVERT: C 1051 MET cc_start: 0.9131 (tpt) cc_final: 0.8889 (mmm) REVERT: D 143 MET cc_start: 0.9503 (mtp) cc_final: 0.9248 (mtp) REVERT: D 155 MET cc_start: 0.9163 (tmm) cc_final: 0.8902 (tpt) REVERT: D 256 MET cc_start: 0.8124 (ttm) cc_final: 0.7466 (mtp) REVERT: D 327 MET cc_start: 0.8714 (tpt) cc_final: 0.8417 (tpt) REVERT: D 373 MET cc_start: 0.8837 (mtp) cc_final: 0.8563 (ptp) REVERT: D 516 LEU cc_start: 0.9519 (OUTLIER) cc_final: 0.9119 (pt) REVERT: D 581 MET cc_start: 0.9006 (pmm) cc_final: 0.8621 (pmm) REVERT: D 733 MET cc_start: 0.8747 (OUTLIER) cc_final: 0.8539 (tmm) REVERT: D 983 MET cc_start: 0.8360 (tpp) cc_final: 0.7848 (tpp) REVERT: D 1012 MET cc_start: 0.8930 (OUTLIER) cc_final: 0.8520 (ppp) REVERT: D 1112 MET cc_start: 0.7761 (mmm) cc_final: 0.7440 (mmm) REVERT: E 41 ASP cc_start: 0.8820 (m-30) cc_final: 0.8582 (m-30) REVERT: E 42 GLU cc_start: 0.9547 (mt-10) cc_final: 0.8893 (tp30) REVERT: F 282 MET cc_start: 0.9280 (mmm) cc_final: 0.8935 (mmm) REVERT: J 69 LEU cc_start: 0.8505 (OUTLIER) cc_final: 0.8281 (tm) REVERT: M 11 TYR cc_start: 0.9070 (t80) cc_final: 0.8274 (t80) outliers start: 73 outliers final: 52 residues processed: 178 average time/residue: 0.1899 time to fit residues: 56.3040 Evaluate side-chains 166 residues out of total 2960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 106 time to evaluate : 1.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 ARG Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 95 MET Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain B residue 70 LYS Chi-restraints excluded: chain B residue 96 TYR Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain B residue 124 HIS Chi-restraints excluded: chain B residue 125 ILE Chi-restraints excluded: chain B residue 147 VAL Chi-restraints excluded: chain B residue 159 ILE Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 224 VAL Chi-restraints excluded: chain C residue 226 ILE Chi-restraints excluded: chain C residue 267 THR Chi-restraints excluded: chain C residue 282 ARG Chi-restraints excluded: chain C residue 288 THR Chi-restraints excluded: chain C residue 296 LEU Chi-restraints excluded: chain C residue 356 THR Chi-restraints excluded: chain C residue 357 VAL Chi-restraints excluded: chain C residue 412 ILE Chi-restraints excluded: chain C residue 584 ARG Chi-restraints excluded: chain C residue 626 VAL Chi-restraints excluded: chain C residue 784 LEU Chi-restraints excluded: chain C residue 839 VAL Chi-restraints excluded: chain C residue 868 LEU Chi-restraints excluded: chain C residue 907 LEU Chi-restraints excluded: chain C residue 936 LEU Chi-restraints excluded: chain C residue 1088 LEU Chi-restraints excluded: chain C residue 1089 LEU Chi-restraints excluded: chain C residue 1131 LEU Chi-restraints excluded: chain C residue 1137 VAL Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 148 LEU Chi-restraints excluded: chain D residue 516 LEU Chi-restraints excluded: chain D residue 543 VAL Chi-restraints excluded: chain D residue 559 MET Chi-restraints excluded: chain D residue 729 VAL Chi-restraints excluded: chain D residue 733 MET Chi-restraints excluded: chain D residue 793 TYR Chi-restraints excluded: chain D residue 991 ILE Chi-restraints excluded: chain D residue 1012 MET Chi-restraints excluded: chain D residue 1233 LEU Chi-restraints excluded: chain E residue 70 GLN Chi-restraints excluded: chain F residue 303 VAL Chi-restraints excluded: chain F residue 328 LEU Chi-restraints excluded: chain F residue 460 LEU Chi-restraints excluded: chain F residue 474 VAL Chi-restraints excluded: chain J residue 5 VAL Chi-restraints excluded: chain J residue 69 LEU Chi-restraints excluded: chain M residue 25 ARG Chi-restraints excluded: chain M residue 27 ILE Chi-restraints excluded: chain M residue 39 VAL Chi-restraints excluded: chain M residue 44 LEU Chi-restraints excluded: chain M residue 67 LEU Chi-restraints excluded: chain M residue 78 HIS Chi-restraints excluded: chain M residue 147 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 358 random chunks: chunk 331 optimal weight: 10.0000 chunk 39 optimal weight: 10.0000 chunk 42 optimal weight: 7.9990 chunk 324 optimal weight: 20.0000 chunk 249 optimal weight: 7.9990 chunk 143 optimal weight: 3.9990 chunk 191 optimal weight: 3.9990 chunk 209 optimal weight: 0.7980 chunk 101 optimal weight: 2.9990 chunk 251 optimal weight: 3.9990 chunk 66 optimal weight: 8.9990 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 419 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 476 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 494 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 674 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.035814 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2655 r_free = 0.2655 target = 0.026387 restraints weight = 253571.299| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2690 r_free = 0.2690 target = 0.027227 restraints weight = 138289.401| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2714 r_free = 0.2714 target = 0.027791 restraints weight = 92364.719| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.2730 r_free = 0.2730 target = 0.028173 restraints weight = 70113.937| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2739 r_free = 0.2739 target = 0.028407 restraints weight = 58429.579| |-----------------------------------------------------------------------------| r_work (final): 0.2719 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2719 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2719 r_free = 0.2719 target_work(ls_wunit_k1) = 0.028 | | occupancies: max = 1.00 min = 0.14 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2719 r_free = 0.2719 target_work(ls_wunit_k1) = 0.028 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2719 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8692 moved from start: 0.2739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 30549 Z= 0.168 Angle : 0.619 13.189 41912 Z= 0.320 Chirality : 0.042 0.199 4775 Planarity : 0.004 0.061 5070 Dihedral : 19.059 176.322 5207 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 10.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.68 % Favored : 94.32 % Rotamer: Outliers : 2.23 % Allowed : 10.18 % Favored : 87.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.35 (0.14), residues: 3488 helix: 1.33 (0.14), residues: 1417 sheet: -0.93 (0.29), residues: 325 loop : -1.46 (0.15), residues: 1746 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG M 109 TYR 0.026 0.001 TYR E 56 PHE 0.015 0.001 PHE D 6 TRP 0.012 0.001 TRP C 70 HIS 0.007 0.001 HIS C 751 Details of bonding type rmsd covalent geometry : bond 0.00359 (30542) covalent geometry : angle 0.61749 (41906) hydrogen bonds : bond 0.03960 ( 1363) hydrogen bonds : angle 4.56410 ( 3794) metal coordination : bond 0.00544 ( 7) metal coordination : angle 3.37231 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6976 Ramachandran restraints generated. 3488 Oldfield, 0 Emsley, 3488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6976 Ramachandran restraints generated. 3488 Oldfield, 0 Emsley, 3488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 2960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 114 time to evaluate : 1.191 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 1 MET cc_start: 0.8539 (tpp) cc_final: 0.7807 (tpp) REVERT: B 70 LYS cc_start: 0.9402 (OUTLIER) cc_final: 0.9047 (ptpp) REVERT: B 173 LYS cc_start: 0.9053 (tptp) cc_final: 0.8668 (tptp) REVERT: B 177 LYS cc_start: 0.8922 (ptmm) cc_final: 0.8306 (ptmm) REVERT: B 191 LYS cc_start: 0.9221 (ttpt) cc_final: 0.9005 (tptt) REVERT: C 103 MET cc_start: 0.9250 (ptm) cc_final: 0.8701 (ppp) REVERT: C 159 MET cc_start: 0.9301 (tpp) cc_final: 0.8878 (mmm) REVERT: C 355 MET cc_start: 0.8808 (tmm) cc_final: 0.8475 (tmm) REVERT: C 393 MET cc_start: 0.9419 (tpp) cc_final: 0.9169 (mmm) REVERT: C 404 MET cc_start: 0.8596 (ptp) cc_final: 0.8288 (ptt) REVERT: C 412 ILE cc_start: 0.9246 (OUTLIER) cc_final: 0.9045 (mm) REVERT: C 586 MET cc_start: 0.9294 (ppp) cc_final: 0.8214 (ppp) REVERT: C 607 MET cc_start: 0.8850 (mtt) cc_final: 0.8463 (mtm) REVERT: C 611 MET cc_start: 0.9152 (mtm) cc_final: 0.8791 (mtp) REVERT: C 630 MET cc_start: 0.8871 (mmm) cc_final: 0.8670 (mmp) REVERT: C 661 MET cc_start: 0.8870 (tpt) cc_final: 0.8521 (tpt) REVERT: C 784 LEU cc_start: 0.9382 (OUTLIER) cc_final: 0.9028 (pp) REVERT: C 907 LEU cc_start: 0.9306 (OUTLIER) cc_final: 0.9068 (tm) REVERT: C 1051 MET cc_start: 0.9074 (tpt) cc_final: 0.8861 (mmm) REVERT: C 1071 MET cc_start: 0.9223 (mtp) cc_final: 0.8996 (mtp) REVERT: C 1076 MET cc_start: 0.9401 (mmm) cc_final: 0.8892 (mmm) REVERT: D 143 MET cc_start: 0.9473 (mtp) cc_final: 0.9244 (mtp) REVERT: D 155 MET cc_start: 0.9104 (tmm) cc_final: 0.8867 (tpt) REVERT: D 256 MET cc_start: 0.8182 (ttm) cc_final: 0.7574 (mtp) REVERT: D 327 MET cc_start: 0.8731 (tpt) cc_final: 0.8511 (tpt) REVERT: D 373 MET cc_start: 0.8786 (mtp) cc_final: 0.8501 (ptp) REVERT: D 516 LEU cc_start: 0.9475 (OUTLIER) cc_final: 0.9085 (pt) REVERT: D 581 MET cc_start: 0.9001 (pmm) cc_final: 0.8653 (pmm) REVERT: D 706 MET cc_start: 0.9173 (mmm) cc_final: 0.8860 (mmm) REVERT: D 1012 MET cc_start: 0.8924 (OUTLIER) cc_final: 0.8531 (ppp) REVERT: D 1112 MET cc_start: 0.7794 (mmm) cc_final: 0.7474 (mmm) REVERT: E 41 ASP cc_start: 0.8830 (m-30) cc_final: 0.8565 (m-30) REVERT: E 42 GLU cc_start: 0.9528 (mt-10) cc_final: 0.8887 (tp30) REVERT: F 282 MET cc_start: 0.9378 (mmm) cc_final: 0.9026 (mmm) REVERT: J 60 MET cc_start: 0.8482 (ppp) cc_final: 0.7239 (ppp) REVERT: J 69 LEU cc_start: 0.8573 (OUTLIER) cc_final: 0.8371 (tm) REVERT: M 11 TYR cc_start: 0.9051 (t80) cc_final: 0.8291 (t80) outliers start: 65 outliers final: 45 residues processed: 172 average time/residue: 0.1904 time to fit residues: 54.4778 Evaluate side-chains 158 residues out of total 2960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 106 time to evaluate : 1.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 ARG Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 95 MET Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain B residue 70 LYS Chi-restraints excluded: chain B residue 96 TYR Chi-restraints excluded: chain B residue 124 HIS Chi-restraints excluded: chain B residue 125 ILE Chi-restraints excluded: chain B residue 147 VAL Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 93 LEU Chi-restraints excluded: chain C residue 224 VAL Chi-restraints excluded: chain C residue 226 ILE Chi-restraints excluded: chain C residue 250 GLU Chi-restraints excluded: chain C residue 267 THR Chi-restraints excluded: chain C residue 282 ARG Chi-restraints excluded: chain C residue 288 THR Chi-restraints excluded: chain C residue 356 THR Chi-restraints excluded: chain C residue 357 VAL Chi-restraints excluded: chain C residue 412 ILE Chi-restraints excluded: chain C residue 584 ARG Chi-restraints excluded: chain C residue 626 VAL Chi-restraints excluded: chain C residue 784 LEU Chi-restraints excluded: chain C residue 839 VAL Chi-restraints excluded: chain C residue 868 LEU Chi-restraints excluded: chain C residue 907 LEU Chi-restraints excluded: chain C residue 936 LEU Chi-restraints excluded: chain C residue 1089 LEU Chi-restraints excluded: chain C residue 1131 LEU Chi-restraints excluded: chain C residue 1137 VAL Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 148 LEU Chi-restraints excluded: chain D residue 516 LEU Chi-restraints excluded: chain D residue 543 VAL Chi-restraints excluded: chain D residue 729 VAL Chi-restraints excluded: chain D residue 793 TYR Chi-restraints excluded: chain D residue 983 MET Chi-restraints excluded: chain D residue 1012 MET Chi-restraints excluded: chain F residue 303 VAL Chi-restraints excluded: chain F residue 328 LEU Chi-restraints excluded: chain F residue 460 LEU Chi-restraints excluded: chain F residue 474 VAL Chi-restraints excluded: chain J residue 5 VAL Chi-restraints excluded: chain J residue 69 LEU Chi-restraints excluded: chain M residue 25 ARG Chi-restraints excluded: chain M residue 27 ILE Chi-restraints excluded: chain M residue 39 VAL Chi-restraints excluded: chain M residue 44 LEU Chi-restraints excluded: chain M residue 67 LEU Chi-restraints excluded: chain M residue 78 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 358 random chunks: chunk 158 optimal weight: 10.0000 chunk 69 optimal weight: 0.7980 chunk 41 optimal weight: 5.9990 chunk 283 optimal weight: 3.9990 chunk 147 optimal weight: 10.0000 chunk 75 optimal weight: 8.9990 chunk 77 optimal weight: 3.9990 chunk 281 optimal weight: 9.9990 chunk 270 optimal weight: 10.0000 chunk 194 optimal weight: 9.9990 chunk 36 optimal weight: 6.9990 overall best weight: 4.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 419 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 476 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 479 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 841 HIS ** D 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 494 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 674 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.035499 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.2640 r_free = 0.2640 target = 0.026093 restraints weight = 255574.641| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.2675 r_free = 0.2675 target = 0.026924 restraints weight = 140299.406| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2699 r_free = 0.2699 target = 0.027480 restraints weight = 94183.600| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.2715 r_free = 0.2715 target = 0.027866 restraints weight = 71673.784| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2724 r_free = 0.2724 target = 0.028100 restraints weight = 59438.447| |-----------------------------------------------------------------------------| r_work (final): 0.2703 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2704 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2704 r_free = 0.2704 target_work(ls_wunit_k1) = 0.028 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2704 r_free = 0.2704 target_work(ls_wunit_k1) = 0.028 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2704 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8708 moved from start: 0.2897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 30549 Z= 0.212 Angle : 0.643 10.865 41912 Z= 0.332 Chirality : 0.042 0.182 4775 Planarity : 0.004 0.064 5070 Dihedral : 19.050 176.400 5207 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 11.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.62 % Favored : 94.38 % Rotamer: Outliers : 2.50 % Allowed : 10.32 % Favored : 87.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.31 (0.15), residues: 3488 helix: 1.36 (0.14), residues: 1415 sheet: -0.90 (0.29), residues: 325 loop : -1.44 (0.15), residues: 1748 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 301 TYR 0.026 0.001 TYR E 56 PHE 0.020 0.001 PHE C 61 TRP 0.012 0.001 TRP C 70 HIS 0.006 0.001 HIS C 751 Details of bonding type rmsd covalent geometry : bond 0.00448 (30542) covalent geometry : angle 0.64218 (41906) hydrogen bonds : bond 0.04229 ( 1363) hydrogen bonds : angle 4.61302 ( 3794) metal coordination : bond 0.00797 ( 7) metal coordination : angle 3.44295 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6976 Ramachandran restraints generated. 3488 Oldfield, 0 Emsley, 3488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6976 Ramachandran restraints generated. 3488 Oldfield, 0 Emsley, 3488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 2960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 107 time to evaluate : 1.257 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 1 MET cc_start: 0.8585 (tpp) cc_final: 0.7822 (tpp) REVERT: B 70 LYS cc_start: 0.9411 (OUTLIER) cc_final: 0.9050 (ptpp) REVERT: B 173 LYS cc_start: 0.9043 (tptp) cc_final: 0.8691 (tptp) REVERT: B 177 LYS cc_start: 0.8921 (ptmm) cc_final: 0.8327 (ptmm) REVERT: B 191 LYS cc_start: 0.9211 (ttpt) cc_final: 0.8607 (tttp) REVERT: C 103 MET cc_start: 0.9271 (ptm) cc_final: 0.8700 (ppp) REVERT: C 159 MET cc_start: 0.9326 (tpp) cc_final: 0.8868 (mmm) REVERT: C 355 MET cc_start: 0.8845 (tmm) cc_final: 0.8605 (tmm) REVERT: C 393 MET cc_start: 0.9428 (tpp) cc_final: 0.9164 (mmm) REVERT: C 404 MET cc_start: 0.8670 (ptp) cc_final: 0.8431 (ptt) REVERT: C 586 MET cc_start: 0.9312 (ppp) cc_final: 0.8239 (ppp) REVERT: C 607 MET cc_start: 0.8862 (mtt) cc_final: 0.8451 (mtm) REVERT: C 611 MET cc_start: 0.9189 (mtm) cc_final: 0.8814 (mtp) REVERT: C 661 MET cc_start: 0.8884 (tpt) cc_final: 0.8504 (tpt) REVERT: C 784 LEU cc_start: 0.9425 (OUTLIER) cc_final: 0.9070 (pp) REVERT: C 907 LEU cc_start: 0.9363 (OUTLIER) cc_final: 0.9123 (tm) REVERT: C 1051 MET cc_start: 0.9167 (tpt) cc_final: 0.8927 (mmm) REVERT: C 1089 LEU cc_start: 0.9751 (OUTLIER) cc_final: 0.9531 (mp) REVERT: D 256 MET cc_start: 0.8191 (ttm) cc_final: 0.7551 (mtp) REVERT: D 327 MET cc_start: 0.8748 (tpt) cc_final: 0.8531 (tmm) REVERT: D 457 MET cc_start: 0.9313 (mtp) cc_final: 0.9035 (mmm) REVERT: D 516 LEU cc_start: 0.9435 (OUTLIER) cc_final: 0.9125 (pp) REVERT: D 581 MET cc_start: 0.9002 (pmm) cc_final: 0.8615 (pmm) REVERT: D 706 MET cc_start: 0.9202 (mmm) cc_final: 0.8944 (mmm) REVERT: D 975 CYS cc_start: 0.9120 (OUTLIER) cc_final: 0.8743 (p) REVERT: D 983 MET cc_start: 0.8300 (OUTLIER) cc_final: 0.7754 (tpp) REVERT: D 1012 MET cc_start: 0.8875 (OUTLIER) cc_final: 0.8507 (ppp) REVERT: D 1112 MET cc_start: 0.7813 (mmm) cc_final: 0.7490 (mmm) REVERT: E 42 GLU cc_start: 0.9545 (mt-10) cc_final: 0.8911 (tp30) REVERT: J 60 MET cc_start: 0.8462 (ppp) cc_final: 0.7220 (ppp) REVERT: M 11 TYR cc_start: 0.9049 (t80) cc_final: 0.8301 (t80) outliers start: 73 outliers final: 49 residues processed: 170 average time/residue: 0.1929 time to fit residues: 54.4843 Evaluate side-chains 162 residues out of total 2960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 105 time to evaluate : 1.109 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 ARG Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 95 MET Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain B residue 70 LYS Chi-restraints excluded: chain B residue 96 TYR Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain B residue 124 HIS Chi-restraints excluded: chain B residue 125 ILE Chi-restraints excluded: chain B residue 147 VAL Chi-restraints excluded: chain B residue 159 ILE Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 224 VAL Chi-restraints excluded: chain C residue 226 ILE Chi-restraints excluded: chain C residue 250 GLU Chi-restraints excluded: chain C residue 267 THR Chi-restraints excluded: chain C residue 282 ARG Chi-restraints excluded: chain C residue 288 THR Chi-restraints excluded: chain C residue 296 LEU Chi-restraints excluded: chain C residue 357 VAL Chi-restraints excluded: chain C residue 584 ARG Chi-restraints excluded: chain C residue 626 VAL Chi-restraints excluded: chain C residue 784 LEU Chi-restraints excluded: chain C residue 839 VAL Chi-restraints excluded: chain C residue 868 LEU Chi-restraints excluded: chain C residue 907 LEU Chi-restraints excluded: chain C residue 936 LEU Chi-restraints excluded: chain C residue 1088 LEU Chi-restraints excluded: chain C residue 1089 LEU Chi-restraints excluded: chain C residue 1131 LEU Chi-restraints excluded: chain C residue 1137 VAL Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 148 LEU Chi-restraints excluded: chain D residue 516 LEU Chi-restraints excluded: chain D residue 543 VAL Chi-restraints excluded: chain D residue 559 MET Chi-restraints excluded: chain D residue 729 VAL Chi-restraints excluded: chain D residue 793 TYR Chi-restraints excluded: chain D residue 975 CYS Chi-restraints excluded: chain D residue 983 MET Chi-restraints excluded: chain D residue 1012 MET Chi-restraints excluded: chain D residue 1233 LEU Chi-restraints excluded: chain F residue 303 VAL Chi-restraints excluded: chain F residue 328 LEU Chi-restraints excluded: chain F residue 460 LEU Chi-restraints excluded: chain F residue 474 VAL Chi-restraints excluded: chain J residue 5 VAL Chi-restraints excluded: chain M residue 25 ARG Chi-restraints excluded: chain M residue 27 ILE Chi-restraints excluded: chain M residue 39 VAL Chi-restraints excluded: chain M residue 44 LEU Chi-restraints excluded: chain M residue 67 LEU Chi-restraints excluded: chain M residue 78 HIS Chi-restraints excluded: chain M residue 147 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 358 random chunks: chunk 217 optimal weight: 5.9990 chunk 159 optimal weight: 0.9980 chunk 29 optimal weight: 5.9990 chunk 243 optimal weight: 10.0000 chunk 126 optimal weight: 10.0000 chunk 24 optimal weight: 4.9990 chunk 144 optimal weight: 0.8980 chunk 247 optimal weight: 0.0370 chunk 104 optimal weight: 6.9990 chunk 15 optimal weight: 10.0000 chunk 333 optimal weight: 10.0000 overall best weight: 2.5862 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 372 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 419 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 476 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 479 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 494 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.036052 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2663 r_free = 0.2663 target = 0.026603 restraints weight = 252844.313| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2698 r_free = 0.2698 target = 0.027441 restraints weight = 139469.052| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2721 r_free = 0.2721 target = 0.028006 restraints weight = 93751.956| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2735 r_free = 0.2735 target = 0.028333 restraints weight = 71381.424| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.2747 r_free = 0.2747 target = 0.028632 restraints weight = 60412.544| |-----------------------------------------------------------------------------| r_work (final): 0.2725 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2726 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2726 r_free = 0.2726 target_work(ls_wunit_k1) = 0.028 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2726 r_free = 0.2726 target_work(ls_wunit_k1) = 0.028 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2726 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8682 moved from start: 0.2987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 30549 Z= 0.148 Angle : 0.617 11.060 41912 Z= 0.315 Chirality : 0.041 0.243 4775 Planarity : 0.004 0.061 5070 Dihedral : 19.000 176.196 5207 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 9.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer: Outliers : 1.95 % Allowed : 10.94 % Favored : 87.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.15 (0.15), residues: 3488 helix: 1.48 (0.14), residues: 1415 sheet: -0.88 (0.29), residues: 333 loop : -1.32 (0.15), residues: 1740 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 77 TYR 0.022 0.001 TYR E 56 PHE 0.022 0.001 PHE C 61 TRP 0.013 0.001 TRP D 223 HIS 0.005 0.001 HIS C 751 Details of bonding type rmsd covalent geometry : bond 0.00319 (30542) covalent geometry : angle 0.61565 (41906) hydrogen bonds : bond 0.03688 ( 1363) hydrogen bonds : angle 4.43883 ( 3794) metal coordination : bond 0.00436 ( 7) metal coordination : angle 3.13554 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6976 Ramachandran restraints generated. 3488 Oldfield, 0 Emsley, 3488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6976 Ramachandran restraints generated. 3488 Oldfield, 0 Emsley, 3488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 2960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 112 time to evaluate : 1.169 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 1 MET cc_start: 0.8562 (tpp) cc_final: 0.7850 (tpp) REVERT: B 70 LYS cc_start: 0.9428 (OUTLIER) cc_final: 0.9082 (pttt) REVERT: B 173 LYS cc_start: 0.9045 (tptp) cc_final: 0.8812 (tptp) REVERT: B 177 LYS cc_start: 0.8871 (ptmm) cc_final: 0.8286 (ptmm) REVERT: B 191 LYS cc_start: 0.9193 (ttpt) cc_final: 0.8587 (tttp) REVERT: C 103 MET cc_start: 0.9276 (ptm) cc_final: 0.8706 (ppp) REVERT: C 159 MET cc_start: 0.9285 (tpp) cc_final: 0.8839 (mmm) REVERT: C 282 ARG cc_start: 0.5674 (OUTLIER) cc_final: 0.5266 (pmm-80) REVERT: C 355 MET cc_start: 0.8983 (tmm) cc_final: 0.8674 (tmm) REVERT: C 393 MET cc_start: 0.9432 (tpp) cc_final: 0.9160 (mmm) REVERT: C 404 MET cc_start: 0.8614 (ptp) cc_final: 0.8319 (ptt) REVERT: C 586 MET cc_start: 0.9336 (ppp) cc_final: 0.8276 (ppp) REVERT: C 607 MET cc_start: 0.8874 (mtt) cc_final: 0.8454 (mtm) REVERT: C 611 MET cc_start: 0.9185 (mtm) cc_final: 0.8818 (mtp) REVERT: C 661 MET cc_start: 0.8906 (tpt) cc_final: 0.8517 (tpt) REVERT: C 907 LEU cc_start: 0.9299 (OUTLIER) cc_final: 0.9049 (tm) REVERT: C 1089 LEU cc_start: 0.9758 (OUTLIER) cc_final: 0.9549 (mp) REVERT: D 256 MET cc_start: 0.8174 (ttm) cc_final: 0.7542 (mtp) REVERT: D 327 MET cc_start: 0.8773 (tpt) cc_final: 0.8521 (mmm) REVERT: D 373 MET cc_start: 0.8783 (ptm) cc_final: 0.8513 (ptp) REVERT: D 457 MET cc_start: 0.9341 (mtp) cc_final: 0.8680 (mmm) REVERT: D 516 LEU cc_start: 0.9458 (OUTLIER) cc_final: 0.9097 (pp) REVERT: D 581 MET cc_start: 0.9032 (pmm) cc_final: 0.8657 (pmm) REVERT: D 1012 MET cc_start: 0.8750 (OUTLIER) cc_final: 0.8404 (ppp) REVERT: D 1112 MET cc_start: 0.7713 (mmm) cc_final: 0.7421 (mmm) REVERT: E 42 GLU cc_start: 0.9537 (mt-10) cc_final: 0.8889 (tp30) REVERT: F 282 MET cc_start: 0.9149 (mmp) cc_final: 0.8798 (mmp) REVERT: J 60 MET cc_start: 0.8464 (ppp) cc_final: 0.7202 (ppp) REVERT: M 11 TYR cc_start: 0.9071 (t80) cc_final: 0.8331 (t80) outliers start: 57 outliers final: 41 residues processed: 160 average time/residue: 0.2048 time to fit residues: 53.6347 Evaluate side-chains 155 residues out of total 2960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 108 time to evaluate : 1.146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 ARG Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 95 MET Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain B residue 70 LYS Chi-restraints excluded: chain B residue 96 TYR Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain B residue 124 HIS Chi-restraints excluded: chain B residue 125 ILE Chi-restraints excluded: chain B residue 147 VAL Chi-restraints excluded: chain C residue 77 ARG Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 224 VAL Chi-restraints excluded: chain C residue 250 GLU Chi-restraints excluded: chain C residue 267 THR Chi-restraints excluded: chain C residue 282 ARG Chi-restraints excluded: chain C residue 288 THR Chi-restraints excluded: chain C residue 357 VAL Chi-restraints excluded: chain C residue 584 ARG Chi-restraints excluded: chain C residue 626 VAL Chi-restraints excluded: chain C residue 839 VAL Chi-restraints excluded: chain C residue 868 LEU Chi-restraints excluded: chain C residue 907 LEU Chi-restraints excluded: chain C residue 936 LEU Chi-restraints excluded: chain C residue 1089 LEU Chi-restraints excluded: chain C residue 1131 LEU Chi-restraints excluded: chain C residue 1137 VAL Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 148 LEU Chi-restraints excluded: chain D residue 516 LEU Chi-restraints excluded: chain D residue 543 VAL Chi-restraints excluded: chain D residue 729 VAL Chi-restraints excluded: chain D residue 793 TYR Chi-restraints excluded: chain D residue 983 MET Chi-restraints excluded: chain D residue 1012 MET Chi-restraints excluded: chain F residue 303 VAL Chi-restraints excluded: chain F residue 328 LEU Chi-restraints excluded: chain F residue 460 LEU Chi-restraints excluded: chain J residue 5 VAL Chi-restraints excluded: chain M residue 25 ARG Chi-restraints excluded: chain M residue 27 ILE Chi-restraints excluded: chain M residue 67 LEU Chi-restraints excluded: chain M residue 78 HIS Chi-restraints excluded: chain M residue 158 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 358 random chunks: chunk 23 optimal weight: 10.0000 chunk 102 optimal weight: 7.9990 chunk 95 optimal weight: 2.9990 chunk 6 optimal weight: 0.9980 chunk 230 optimal weight: 2.9990 chunk 72 optimal weight: 9.9990 chunk 305 optimal weight: 10.0000 chunk 138 optimal weight: 10.0000 chunk 303 optimal weight: 9.9990 chunk 241 optimal weight: 0.9990 chunk 131 optimal weight: 6.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 124 HIS ** C 419 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 479 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 494 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 674 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.035999 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2659 r_free = 0.2659 target = 0.026525 restraints weight = 252992.492| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2695 r_free = 0.2695 target = 0.027371 restraints weight = 138644.952| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2718 r_free = 0.2718 target = 0.027941 restraints weight = 92866.643| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.2734 r_free = 0.2734 target = 0.028320 restraints weight = 70659.191| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2743 r_free = 0.2743 target = 0.028555 restraints weight = 58987.579| |-----------------------------------------------------------------------------| r_work (final): 0.2723 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2723 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2723 r_free = 0.2723 target_work(ls_wunit_k1) = 0.028 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2723 r_free = 0.2723 target_work(ls_wunit_k1) = 0.028 | | occupancies: max = 1.00 min = 0.14 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2723 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8689 moved from start: 0.3086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 30549 Z= 0.163 Angle : 0.628 11.449 41912 Z= 0.320 Chirality : 0.041 0.249 4775 Planarity : 0.004 0.061 5070 Dihedral : 18.966 176.025 5207 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 10.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.36 % Favored : 94.64 % Rotamer: Outliers : 1.99 % Allowed : 11.11 % Favored : 86.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.16 (0.15), residues: 3488 helix: 1.45 (0.14), residues: 1422 sheet: -0.83 (0.29), residues: 337 loop : -1.32 (0.15), residues: 1729 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 77 TYR 0.031 0.001 TYR E 67 PHE 0.019 0.001 PHE C 61 TRP 0.012 0.001 TRP D 223 HIS 0.005 0.001 HIS C 751 Details of bonding type rmsd covalent geometry : bond 0.00350 (30542) covalent geometry : angle 0.62686 (41906) hydrogen bonds : bond 0.03756 ( 1363) hydrogen bonds : angle 4.45779 ( 3794) metal coordination : bond 0.00524 ( 7) metal coordination : angle 3.02026 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6976 Ramachandran restraints generated. 3488 Oldfield, 0 Emsley, 3488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6976 Ramachandran restraints generated. 3488 Oldfield, 0 Emsley, 3488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 2960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 111 time to evaluate : 1.200 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 1 MET cc_start: 0.8555 (tpp) cc_final: 0.7837 (tpp) REVERT: B 70 LYS cc_start: 0.9413 (OUTLIER) cc_final: 0.9101 (pttt) REVERT: B 177 LYS cc_start: 0.8880 (ptmm) cc_final: 0.8243 (ptmm) REVERT: B 191 LYS cc_start: 0.9202 (ttpt) cc_final: 0.8955 (ttpp) REVERT: C 103 MET cc_start: 0.9208 (ptm) cc_final: 0.8645 (ppp) REVERT: C 159 MET cc_start: 0.9254 (tpp) cc_final: 0.8815 (mmm) REVERT: C 282 ARG cc_start: 0.6073 (OUTLIER) cc_final: 0.5728 (pmm-80) REVERT: C 393 MET cc_start: 0.9443 (tpp) cc_final: 0.9171 (mmm) REVERT: C 404 MET cc_start: 0.8637 (ptp) cc_final: 0.8426 (ptp) REVERT: C 586 MET cc_start: 0.9348 (ppp) cc_final: 0.8282 (ppp) REVERT: C 607 MET cc_start: 0.8865 (mtt) cc_final: 0.8446 (mtm) REVERT: C 611 MET cc_start: 0.9172 (mtm) cc_final: 0.8818 (mtp) REVERT: C 661 MET cc_start: 0.8819 (tpt) cc_final: 0.8427 (tpt) REVERT: C 784 LEU cc_start: 0.9410 (OUTLIER) cc_final: 0.9049 (pp) REVERT: C 907 LEU cc_start: 0.9309 (OUTLIER) cc_final: 0.9064 (tm) REVERT: C 926 MET cc_start: 0.8974 (tpp) cc_final: 0.8524 (tpp) REVERT: D 155 MET cc_start: 0.9059 (tmm) cc_final: 0.8795 (tpt) REVERT: D 256 MET cc_start: 0.8206 (ttm) cc_final: 0.7546 (mtp) REVERT: D 327 MET cc_start: 0.8787 (tpt) cc_final: 0.8534 (mmm) REVERT: D 373 MET cc_start: 0.8750 (ptm) cc_final: 0.8492 (ptp) REVERT: D 457 MET cc_start: 0.9362 (mtp) cc_final: 0.8835 (mmt) REVERT: D 516 LEU cc_start: 0.9452 (OUTLIER) cc_final: 0.9095 (pp) REVERT: D 581 MET cc_start: 0.9004 (pmm) cc_final: 0.8631 (pmm) REVERT: D 1012 MET cc_start: 0.8701 (OUTLIER) cc_final: 0.8357 (ppp) REVERT: D 1112 MET cc_start: 0.7813 (mmm) cc_final: 0.7496 (mmm) REVERT: E 41 ASP cc_start: 0.9031 (m-30) cc_final: 0.8734 (p0) REVERT: E 42 GLU cc_start: 0.9533 (mt-10) cc_final: 0.8918 (tp30) REVERT: F 281 MET cc_start: 0.8909 (ptp) cc_final: 0.8579 (pmm) REVERT: F 282 MET cc_start: 0.9101 (mmp) cc_final: 0.8609 (mmp) REVERT: J 60 MET cc_start: 0.8448 (ppp) cc_final: 0.7182 (ppp) REVERT: M 11 TYR cc_start: 0.9060 (t80) cc_final: 0.8319 (t80) outliers start: 58 outliers final: 43 residues processed: 160 average time/residue: 0.2097 time to fit residues: 54.4602 Evaluate side-chains 160 residues out of total 2960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 111 time to evaluate : 1.050 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 ARG Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 95 MET Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain B residue 70 LYS Chi-restraints excluded: chain B residue 96 TYR Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain B residue 125 ILE Chi-restraints excluded: chain B residue 147 VAL Chi-restraints excluded: chain C residue 77 ARG Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 224 VAL Chi-restraints excluded: chain C residue 226 ILE Chi-restraints excluded: chain C residue 250 GLU Chi-restraints excluded: chain C residue 267 THR Chi-restraints excluded: chain C residue 282 ARG Chi-restraints excluded: chain C residue 288 THR Chi-restraints excluded: chain C residue 357 VAL Chi-restraints excluded: chain C residue 584 ARG Chi-restraints excluded: chain C residue 626 VAL Chi-restraints excluded: chain C residue 784 LEU Chi-restraints excluded: chain C residue 839 VAL Chi-restraints excluded: chain C residue 868 LEU Chi-restraints excluded: chain C residue 907 LEU Chi-restraints excluded: chain C residue 936 LEU Chi-restraints excluded: chain C residue 1131 LEU Chi-restraints excluded: chain C residue 1137 VAL Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 148 LEU Chi-restraints excluded: chain D residue 516 LEU Chi-restraints excluded: chain D residue 543 VAL Chi-restraints excluded: chain D residue 559 MET Chi-restraints excluded: chain D residue 729 VAL Chi-restraints excluded: chain D residue 793 TYR Chi-restraints excluded: chain D residue 983 MET Chi-restraints excluded: chain D residue 1012 MET Chi-restraints excluded: chain F residue 303 VAL Chi-restraints excluded: chain F residue 328 LEU Chi-restraints excluded: chain F residue 460 LEU Chi-restraints excluded: chain J residue 5 VAL Chi-restraints excluded: chain M residue 25 ARG Chi-restraints excluded: chain M residue 27 ILE Chi-restraints excluded: chain M residue 39 VAL Chi-restraints excluded: chain M residue 67 LEU Chi-restraints excluded: chain M residue 78 HIS Chi-restraints excluded: chain M residue 158 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 358 random chunks: chunk 56 optimal weight: 3.9990 chunk 105 optimal weight: 5.9990 chunk 294 optimal weight: 0.3980 chunk 221 optimal weight: 0.9990 chunk 20 optimal weight: 10.0000 chunk 145 optimal weight: 9.9990 chunk 271 optimal weight: 9.9990 chunk 291 optimal weight: 7.9990 chunk 166 optimal weight: 0.8980 chunk 296 optimal weight: 9.9990 chunk 41 optimal weight: 6.9990 overall best weight: 2.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 124 HIS ** C 419 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 479 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 494 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 674 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1001 GLN ** D1110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 106 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.036309 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2677 r_free = 0.2677 target = 0.026866 restraints weight = 253685.158| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.2711 r_free = 0.2711 target = 0.027698 restraints weight = 139985.773| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.2735 r_free = 0.2735 target = 0.028267 restraints weight = 94276.415| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.2750 r_free = 0.2750 target = 0.028637 restraints weight = 71809.096| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2759 r_free = 0.2759 target = 0.028875 restraints weight = 59963.672| |-----------------------------------------------------------------------------| r_work (final): 0.2738 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2739 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2739 r_free = 0.2739 target_work(ls_wunit_k1) = 0.028 | | occupancies: max = 1.00 min = 0.14 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2739 r_free = 0.2739 target_work(ls_wunit_k1) = 0.028 | | occupancies: max = 1.00 min = 0.09 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.2739 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8676 moved from start: 0.3201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 30549 Z= 0.144 Angle : 0.619 13.315 41912 Z= 0.313 Chirality : 0.041 0.239 4775 Planarity : 0.004 0.061 5070 Dihedral : 18.932 176.501 5207 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 9.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 1.99 % Allowed : 11.11 % Favored : 86.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.07 (0.15), residues: 3488 helix: 1.52 (0.14), residues: 1422 sheet: -0.71 (0.29), residues: 325 loop : -1.29 (0.15), residues: 1741 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 77 TYR 0.022 0.001 TYR E 56 PHE 0.018 0.001 PHE C 61 TRP 0.013 0.001 TRP D 223 HIS 0.005 0.001 HIS C 751 Details of bonding type rmsd covalent geometry : bond 0.00312 (30542) covalent geometry : angle 0.61768 (41906) hydrogen bonds : bond 0.03510 ( 1363) hydrogen bonds : angle 4.37207 ( 3794) metal coordination : bond 0.00409 ( 7) metal coordination : angle 2.88967 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6976 Ramachandran restraints generated. 3488 Oldfield, 0 Emsley, 3488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6976 Ramachandran restraints generated. 3488 Oldfield, 0 Emsley, 3488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 2960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 113 time to evaluate : 1.249 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 1 MET cc_start: 0.8614 (tpp) cc_final: 0.7887 (tpp) REVERT: B 70 LYS cc_start: 0.9404 (OUTLIER) cc_final: 0.9104 (pttm) REVERT: B 173 LYS cc_start: 0.9092 (tptp) cc_final: 0.8841 (tptp) REVERT: B 177 LYS cc_start: 0.8831 (ptmm) cc_final: 0.8194 (ptmm) REVERT: B 191 LYS cc_start: 0.9188 (ttpt) cc_final: 0.8942 (ttpp) REVERT: C 103 MET cc_start: 0.9115 (ptm) cc_final: 0.8513 (ppp) REVERT: C 159 MET cc_start: 0.9248 (tpp) cc_final: 0.8840 (mmm) REVERT: C 282 ARG cc_start: 0.6371 (OUTLIER) cc_final: 0.5982 (pmm-80) REVERT: C 393 MET cc_start: 0.9429 (tpp) cc_final: 0.9119 (mmm) REVERT: C 586 MET cc_start: 0.9360 (ppp) cc_final: 0.8300 (ppp) REVERT: C 607 MET cc_start: 0.8854 (mtt) cc_final: 0.8443 (mtm) REVERT: C 611 MET cc_start: 0.9166 (mtm) cc_final: 0.8711 (ptp) REVERT: C 661 MET cc_start: 0.8767 (tpt) cc_final: 0.8385 (tpt) REVERT: C 784 LEU cc_start: 0.9407 (OUTLIER) cc_final: 0.9046 (pp) REVERT: C 907 LEU cc_start: 0.9303 (OUTLIER) cc_final: 0.9050 (tm) REVERT: C 926 MET cc_start: 0.8981 (tpp) cc_final: 0.8542 (tpp) REVERT: D 155 MET cc_start: 0.9109 (tmm) cc_final: 0.8819 (tpt) REVERT: D 256 MET cc_start: 0.8203 (ttm) cc_final: 0.7523 (mtp) REVERT: D 327 MET cc_start: 0.8806 (tpt) cc_final: 0.8550 (mmm) REVERT: D 373 MET cc_start: 0.8768 (ptm) cc_final: 0.8488 (ptp) REVERT: D 447 MET cc_start: 0.9179 (ttp) cc_final: 0.8978 (ptm) REVERT: D 457 MET cc_start: 0.9363 (mtp) cc_final: 0.8845 (mmt) REVERT: D 516 LEU cc_start: 0.9436 (OUTLIER) cc_final: 0.9079 (pp) REVERT: D 581 MET cc_start: 0.8986 (pmm) cc_final: 0.8615 (pmm) REVERT: D 1012 MET cc_start: 0.8669 (OUTLIER) cc_final: 0.8342 (ppp) REVERT: D 1112 MET cc_start: 0.7788 (mmm) cc_final: 0.7519 (mmm) REVERT: E 42 GLU cc_start: 0.9506 (mt-10) cc_final: 0.8964 (tp30) REVERT: F 281 MET cc_start: 0.8933 (ptp) cc_final: 0.8575 (pmm) REVERT: F 282 MET cc_start: 0.9123 (mmp) cc_final: 0.8596 (mmp) REVERT: J 60 MET cc_start: 0.8404 (ppp) cc_final: 0.7132 (ppp) REVERT: M 11 TYR cc_start: 0.9083 (t80) cc_final: 0.8276 (t80) outliers start: 58 outliers final: 46 residues processed: 162 average time/residue: 0.1991 time to fit residues: 52.5708 Evaluate side-chains 159 residues out of total 2960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 107 time to evaluate : 1.159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 ARG Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 95 MET Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain B residue 70 LYS Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 96 TYR Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain B residue 125 ILE Chi-restraints excluded: chain B residue 147 VAL Chi-restraints excluded: chain C residue 77 ARG Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 224 VAL Chi-restraints excluded: chain C residue 226 ILE Chi-restraints excluded: chain C residue 250 GLU Chi-restraints excluded: chain C residue 267 THR Chi-restraints excluded: chain C residue 282 ARG Chi-restraints excluded: chain C residue 288 THR Chi-restraints excluded: chain C residue 357 VAL Chi-restraints excluded: chain C residue 584 ARG Chi-restraints excluded: chain C residue 626 VAL Chi-restraints excluded: chain C residue 784 LEU Chi-restraints excluded: chain C residue 839 VAL Chi-restraints excluded: chain C residue 868 LEU Chi-restraints excluded: chain C residue 907 LEU Chi-restraints excluded: chain C residue 936 LEU Chi-restraints excluded: chain C residue 1088 LEU Chi-restraints excluded: chain C residue 1131 LEU Chi-restraints excluded: chain C residue 1137 VAL Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 148 LEU Chi-restraints excluded: chain D residue 219 LEU Chi-restraints excluded: chain D residue 516 LEU Chi-restraints excluded: chain D residue 543 VAL Chi-restraints excluded: chain D residue 559 MET Chi-restraints excluded: chain D residue 729 VAL Chi-restraints excluded: chain D residue 793 TYR Chi-restraints excluded: chain D residue 983 MET Chi-restraints excluded: chain D residue 1012 MET Chi-restraints excluded: chain F residue 303 VAL Chi-restraints excluded: chain F residue 328 LEU Chi-restraints excluded: chain F residue 460 LEU Chi-restraints excluded: chain J residue 5 VAL Chi-restraints excluded: chain M residue 25 ARG Chi-restraints excluded: chain M residue 27 ILE Chi-restraints excluded: chain M residue 39 VAL Chi-restraints excluded: chain M residue 67 LEU Chi-restraints excluded: chain M residue 78 HIS Chi-restraints excluded: chain M residue 158 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 358 random chunks: chunk 293 optimal weight: 20.0000 chunk 268 optimal weight: 2.9990 chunk 356 optimal weight: 4.9990 chunk 162 optimal weight: 5.9990 chunk 173 optimal weight: 20.0000 chunk 277 optimal weight: 1.9990 chunk 86 optimal weight: 0.9990 chunk 147 optimal weight: 10.0000 chunk 108 optimal weight: 4.9990 chunk 17 optimal weight: 9.9990 chunk 269 optimal weight: 6.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 124 HIS ** C 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 349 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 419 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 479 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 494 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 674 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.036088 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2670 r_free = 0.2670 target = 0.026650 restraints weight = 256618.847| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2704 r_free = 0.2704 target = 0.027480 restraints weight = 142589.476| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2728 r_free = 0.2728 target = 0.028043 restraints weight = 96063.664| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 50)----------------| | r_work = 0.2743 r_free = 0.2743 target = 0.028424 restraints weight = 73316.151| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2752 r_free = 0.2752 target = 0.028662 restraints weight = 61002.123| |-----------------------------------------------------------------------------| r_work (final): 0.2729 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2730 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2730 r_free = 0.2730 target_work(ls_wunit_k1) = 0.028 | | occupancies: max = 1.00 min = 0.09 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2730 r_free = 0.2730 target_work(ls_wunit_k1) = 0.028 | | occupancies: max = 1.00 min = 0.07 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.2730 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8686 moved from start: 0.3257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 30549 Z= 0.168 Angle : 0.627 11.876 41912 Z= 0.318 Chirality : 0.041 0.260 4775 Planarity : 0.004 0.062 5070 Dihedral : 18.930 176.933 5207 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 10.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.33 % Favored : 94.67 % Rotamer: Outliers : 1.89 % Allowed : 11.21 % Favored : 86.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.07 (0.15), residues: 3488 helix: 1.51 (0.14), residues: 1424 sheet: -0.81 (0.28), residues: 346 loop : -1.25 (0.15), residues: 1718 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG M 109 TYR 0.027 0.001 TYR E 67 PHE 0.017 0.001 PHE C 61 TRP 0.012 0.001 TRP D 223 HIS 0.005 0.001 HIS C 751 Details of bonding type rmsd covalent geometry : bond 0.00359 (30542) covalent geometry : angle 0.62651 (41906) hydrogen bonds : bond 0.03712 ( 1363) hydrogen bonds : angle 4.41700 ( 3794) metal coordination : bond 0.00552 ( 7) metal coordination : angle 2.92188 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4754.77 seconds wall clock time: 83 minutes 6.33 seconds (4986.33 seconds total)